From 6608c4c758066f543901cf6108a35c6bce2b6b25 Mon Sep 17 00:00:00 2001
From: sainsachiko <hthhanh.work@gmail.com>
Date: Sun, 24 May 2026 02:32:11 +0100
Subject: [PATCH 01/20] Test commit: Use new code from this PR

---
 .github/workflows/download_pipeline.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml
index 45884ff9..52784804 100644
--- a/.github/workflows/download_pipeline.yml
+++ b/.github/workflows/download_pipeline.yml
@@ -32,7 +32,7 @@ jobs:
         run: |
           echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> "$GITHUB_OUTPUT"
           echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> "$GITHUB_OUTPUT"
-          echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> "$GITHUB_OUTPUT"
+          echo "REPO_BRANCH=${{ github.event_name == 'pull_request' && github.event.pull_request.head.ref || github.event.inputs.testbranch || 'dev' }}" >> "$GITHUB_OUTPUT"
 
   download:
     runs-on: ubuntu-latest

From aa302afab27d08a5b58b25ad8b025bd3541451dc Mon Sep 17 00:00:00 2001
From: sainsachiko <hthhanh.work@gmail.com>
Date: Thu, 28 May 2026 19:08:03 +0100
Subject: [PATCH 02/20] Add subWF to handle extra_header

---
 subworkflows/local/prepare_read_groups.nf | 64 +++++++++++++++++++++++
 1 file changed, 64 insertions(+)
 create mode 100644 subworkflows/local/prepare_read_groups.nf

diff --git a/subworkflows/local/prepare_read_groups.nf b/subworkflows/local/prepare_read_groups.nf
new file mode 100644
index 00000000..04ff501d
--- /dev/null
+++ b/subworkflows/local/prepare_read_groups.nf
@@ -0,0 +1,64 @@
+//
+// Prepare read-group metadata from optional extra_header and BAM input headers
+//
+
+include { SAMTOOLS_SPLITHEADER } from '../../modules/nf-core/samtools/splitheader/main'
+
+workflow PREPARE_READ_GROUPS {
+    take:
+    reads        // channel: [ val(meta), /path/to/read_file ]
+    rg_mode      // string: read-group mode: 'long' (minimap2 style) or 'short' (samtools addreplacerg style)
+
+    main:
+    // Build mode-specific RG prefix once and reuse it for all reads in this invocation.
+    def rg_lead = rg_mode == 'long' ? '-y' : ''
+    def rg_flag = rg_mode == 'long' ? '-R' : '-r'
+
+    // Pre-populate read_group for all inputs; downstream steps may override it from extracted @RG lines
+    ch_reads_prefixed = reads.map { meta, read_file -> [meta + [read_group: "${rg_lead} ${rg_flag} $meta.read_group", replace_rg: true], read_file] }
+
+    ch_reads_extra_header = ch_reads_prefixed
+        .branch { meta, read_file ->
+            // Inputs with explicit extra_header metadata should be parsed directly
+            has_extra_header: meta.extra_header != []
+                return [meta + [read_file: read_file], meta.extra_header]
+            // For BAM/CRAM without extra_header metadata, extract header from the alignment file.
+            no_extra_header_bam_cram: meta.extra_header == [] && read_file.name ==~ /.*\.(bam|cram)$/
+            // FASTQ and remaining inputs keep the pre-populated read_group.
+            no_extra_header_fastq: true
+        }
+
+    // Extract @RG/@PG from provided extra_header files and BAM/CRAM headers
+    SAMTOOLS_SPLITHEADER(ch_reads_extra_header.has_extra_header.mix(ch_reads_extra_header.no_extra_header_bam_cram))
+
+    ch_reads_with_rg = SAMTOOLS_SPLITHEADER.out.readgroup
+        .join(SAMTOOLS_SPLITHEADER.out.programs)
+        .join(ch_reads_extra_header.has_extra_header.mix(ch_reads_extra_header.no_extra_header_bam_cram), by: 0)
+        .map { meta, rg_file, program_file, read_files ->
+            def rglines = file(rg_file).readLines()
+            // Prefer extracted @RG lines; fallback to the existing read_group only when extraction is empty
+            def rg_args = rglines ? [
+                rg_lead,
+                rglines.collect { line ->
+                    // Add SM when not present to avoid errors from downstream tools (e.g. variant callers)
+                    def l = line.contains('SM:') ? line
+                            : meta.sample ? "${line}\tSM:${meta.sample}"
+                            : "${line}\tSM:${meta.id}"
+                    "${rg_flag} '${l.replaceAll("\t", "\\\\t")}'"
+                }.join(' ')
+            ].findAll { it }.join(' ')
+            : (meta.read_group ?: '')
+
+            def output_read_files = meta.read_file ?: read_files
+            // If RG came from an existing BAM/CRAM header, and no extra RG provided to overwrite, preserve it and avoid replacing downstream
+            // If PG came from an existing BAM/CRAM header, and no extra PG provided to overwrite, preserve it and avoid replacing downstream
+            def replace_rg = !meta.extra_header && rglines ? false : true
+            def add_pg = !meta.extra_header && program_file ? false : true
+            def new_meta = meta.subMap(meta.keySet() - ['read_file']) + [read_group: rg_args, replace_rg: replace_rg, add_pg: add_pg]
+            [new_meta, output_read_files]
+        }
+        .mix(ch_reads_extra_header.no_extra_header_fastq)
+
+    emit:
+    reads = ch_reads_with_rg       // channel: [ val(meta), /path/to/read_file ]
+}

From b281f831ea338ebda3c6ed2099e9656e1274a37d Mon Sep 17 00:00:00 2001
From: sainsachiko <hthhanh.work@gmail.com>
Date: Thu, 28 May 2026 19:09:11 +0100
Subject: [PATCH 03/20] Apply new subWF to handle read_group from extra_header

---
 assets/schema_input.json          |  8 ++++
 conf/modules.config               |  1 +
 modules.json                      |  2 +-
 subworkflows/local/align_long.nf  | 41 +++++-------------
 subworkflows/local/align_short.nf | 71 ++++++++++++++++---------------
 subworkflows/local/input_check.nf |  1 +
 6 files changed, 58 insertions(+), 66 deletions(-)

diff --git a/assets/schema_input.json b/assets/schema_input.json
index 5a4d16de..70754236 100644
--- a/assets/schema_input.json
+++ b/assets/schema_input.json
@@ -45,6 +45,14 @@
                 "errorMessage": "Sample barcode cannot contain spaces",
                 "default": "",
                 "meta": ["barcode"]
+            },
+            "extra_header": {
+                "type": "string",
+                "format": "file-path",
+                "exists": true,
+                "pattern": "^\\S+\\.(sam|sam.gz)$",
+                "errorMessage": "SAM header file cannot contain spaces and must be in SAM format",
+                "meta": ["extra_header"]
             }
         },
         "required": ["specimen", "run", "datatype", "datafile"]
diff --git a/conf/modules.config b/conf/modules.config
index 1c86d8f2..f7f2b817 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -113,6 +113,7 @@ process {
     }
 
     withName: SAMTOOLS_ADDREPLACERG {
+        ext.args =  { "${meta.read_group}" }
         ext.prefix = { "${input.baseName}_addRG" }
     }
 
diff --git a/modules.json b/modules.json
index 979208ba..c00ecfad 100644
--- a/modules.json
+++ b/modules.json
@@ -77,7 +77,7 @@
                     },
                     "samtools/addreplacerg": {
                         "branch": "master",
-                        "git_sha": "156feda0cb6589cd29c04902004fa3b53bc00205",
+                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                         "installed_by": ["modules"]
                     },
                     "samtools/bgzip": {
diff --git a/subworkflows/local/align_long.nf b/subworkflows/local/align_long.nf
index 2f3a8c8f..4982e0d1 100644
--- a/subworkflows/local/align_long.nf
+++ b/subworkflows/local/align_long.nf
@@ -4,6 +4,7 @@
 
 // Include local modules and subworkflows
 include { MERGE_OUTPUT                               } from '../../subworkflows/local/merge_output'
+include { PREPARE_READ_GROUPS                        } from '../../subworkflows/local/prepare_read_groups'
 
 include { PACBIO_PREPROCESS                          } from '../../subworkflows/sanger-tol/pacbio_preprocess/main'
 include { PACBIO_PREPROCESS as PACBIO_PREPROCESS_ULI } from '../../subworkflows/sanger-tol/pacbio_preprocess/main'
@@ -12,7 +13,6 @@ include { FASTX_MAP_LONG_READS                       } from '../../subworkflows/
 // Include nf-core modules
 include { FASTQC as FASTQC_FILTERED                    } from '../../modules/nf-core/fastqc/main'
 include { GAWK as GAWK_MODIFY_YAML_BARCODE             } from '../../modules/nf-core/gawk/main'
-include { SAMTOOLS_SPLITHEADER                         } from '../../modules/nf-core/samtools/splitheader/main'
 include { SAMTOOLS_FASTQ                               } from '../../modules/nf-core/samtools/fastq/main'
 
 workflow ALIGN_LONG {
@@ -30,39 +30,18 @@ workflow ALIGN_LONG {
     //
     // PRESERVE READ GROUP INFORMATION
     //
-    ch_reads_branch = reads
-        .map { meta, read_files -> [meta + [read_group: "-y -R $meta.read_group"], read_files] }
-        .branch { _meta, read_files ->
-            bam: read_files.name.endsWith("bam")
-            fastq: true
-        }
-
-    // Extract read group information from BAM files if BAM files are provided as input
-    SAMTOOLS_SPLITHEADER(ch_reads_branch.bam)
-
-    // Replace constructed read group information with the one extracted from BAM header
-    ch_bam_rg = SAMTOOLS_SPLITHEADER.out.readgroup
-        .join (ch_reads_branch.bam, by:0)
-        .map { meta, rg_file, bam ->
-            def rglines = file(rg_file).readLines()
-            def rg_args = rglines ? '-y ' + rglines.collect { line ->
-                // Add SM when not present to avoid errors from downstream tool (e.g. variant callers)
-                def l = line.contains("SM:") ? line
-                        : meta.sample ? "${line}\tSM:${meta.sample}"
-                        : "${line}\tSM:${meta.id}"
-                    "-R '${l.replaceAll("\t", "\\\\t")}'"
-            }.join(' ')
-            :  meta.read_group
-            [ meta + [read_group:rg_args], bam ]
-        }
-
-    ch_reads_rg = ch_bam_rg.mix( ch_reads_branch.fastq )
+    PREPARE_READ_GROUPS(reads, 'long')
+    ch_read_rg = PREPARE_READ_GROUPS.out.reads
+    ch_read_rg_branch = ch_read_rg.branch { _meta, read_files ->
+        bam: read_files.name.endsWith("bam")
+        fastq: true
+    }
 
     //
     // PACBIO READ PREPROCESSING
     //
     if (val_pacbio_adapter_fasta || val_pacbio_adapter_yaml || val_pacbio_uli_adapter) { // pacbio_adapter_fasta, pacbio_adapter_yaml, pacbio_uli_adapter always provided
-        ch_reads = ch_reads_rg
+        ch_reads = ch_read_rg
             .branch { meta, read_files ->
                 pacbio: meta.datatype == "pacbio"
                 // non pacbio includes ONT and pacbio clr
@@ -144,8 +123,8 @@ workflow ALIGN_LONG {
         fastx = pacbio_fastx.mix( ch_reads.non_pacbio_fastx )
     } else {
         // if no processing needed at all, prepare CRAM for alignment directly from original reads (both pacbio and non-pacbio reads)
-        bam_to_fastx = ch_bam_rg
-        fastx = ch_reads_branch.fastq
+        bam_to_fastx = ch_read_rg_branch.bam
+        fastx = ch_read_rg_branch.fastq
     }
     // readmapping take only 1 FASTA as reference
     SAMTOOLS_FASTQ ( bam_to_fastx, false )
diff --git a/subworkflows/local/align_short.nf b/subworkflows/local/align_short.nf
index 0b035b5e..1b91a437 100644
--- a/subworkflows/local/align_short.nf
+++ b/subworkflows/local/align_short.nf
@@ -2,10 +2,11 @@
 // Align short read (HiC and Illumina) data against the genome
 //
 
-include { CRAM_MAP_ILLUMINA_HIC as CRAM_MAP_ILLUMINA } from '../../subworkflows/sanger-tol/cram_map_illumina_hic'
-include { MERGE_OUTPUT                               } from '../../subworkflows/local/merge_output'
-include { SAMTOOLS_ADDREPLACERG                      } from '../../modules/nf-core/samtools/addreplacerg/main'
-include { SAMTOOLS_VIEW as CONVERT_CRAM              } from '../../modules/nf-core/samtools/view/main'
+include { CRAM_MAP_ILLUMINA_HIC as CRAM_MAP_SHORT_READS } from '../../subworkflows/sanger-tol/cram_map_illumina_hic'
+include { MERGE_OUTPUT                                  } from '../../subworkflows/local/merge_output'
+include { PREPARE_READ_GROUPS                           } from '../../subworkflows/local/prepare_read_groups'
+include { SAMTOOLS_ADDREPLACERG                         } from '../../modules/nf-core/samtools/addreplacerg/main'
+include { SAMTOOLS_VIEW as CONVERT_CRAM                 } from '../../modules/nf-core/samtools/view/main'
 
 workflow ALIGN_SHORT {
     take:
@@ -14,54 +15,56 @@ workflow ALIGN_SHORT {
 
 
     main:
+    //
+    // SUBWORKFLOW: Preserve read-group information from optional extra_header metadata
+    //
+    PREPARE_READ_GROUPS(reads, 'short')
+    reads_with_rg = PREPARE_READ_GROUPS.out.reads
+
+    //
+    // LOGIC: Convert FASTQ to CRAM adn add RG information if needed
+    //
     // Check file types and branch
-    ch_reads = reads
-    .branch {
-        meta, reads_files ->
-            cram : reads_files.findAll { file -> file.name.endsWith(".cram") }
-                [meta + [from: "cram"], reads_files]
-            bam: reads_files.findAll { file -> file.name.endsWith(".bam") }
-                [meta + [from: "bam"], reads_files]
-            fastx: true
-                [meta + [from: "fastx"], reads_files]
+    ch_reads = reads_with_rg.branch { meta, read_files ->
+        cram: read_files.name.endsWith(".cram")
+        non_cram: true
     }
 
-
     // Convert FASTQ to CRAM only if FASTQ were provided as input
-    ch_reads_non_crams = ch_reads.fastx
-        .mix ( ch_reads.bam )
-        .map { meta, file -> [ meta, file, [] ] }
+    ch_reads_non_crams = ch_reads.non_cram.map { meta, file -> [ meta, file, [] ] }
 
     fasta_dummy_idx = fasta.map { meta, fasta_file -> [ meta, fasta_file, [] ] }
     CONVERT_CRAM ( ch_reads_non_crams, fasta_dummy_idx, [[],[]], [[],[]], "" )
 
-    ch_converted_crams = CONVERT_CRAM.out.cram
+    // Add read group information to CRAMs if not already present, and merge with CRAMs that already have RG information
+    ch_crams_to_addrg = CONVERT_CRAM.out.cram
+        .mix ( ch_reads.cram )
         .branch { meta, cram ->
-            with_rg: meta.from == "bam"
-            without_rg: true
+            replace_rg: meta.replace_rg == true
+            not_replace_rg: true
         }
     SAMTOOLS_ADDREPLACERG (
-        ch_converted_crams.without_rg.map{ meta, cram -> [ meta, cram, [], meta.read_group ] },
+        ch_crams_to_addrg.replace_rg.map{ meta, cram -> [ meta, cram, [], [] ] }, // empty value for RG as the modules will use meta.read_group instead (see conf/modules.config)
         [[],[],[],[]]
     )
 
-    ch_reads_cram = SAMTOOLS_ADDREPLACERG.out.cram
-    .mix ( ch_converted_crams.with_rg )
-    .mix ( ch_reads.cram )
-    .map{ meta, cram_file -> [ meta + [ reads_size: cram_file.size() ] , cram_file ] }
-
-    ch_illumina = ch_reads_cram
-    .combine(fasta)
-    .multiMap { meta, cram, meta_, fasta_file ->
-        cram: [ meta_ + meta + [ assembly_id: meta_.id ] , cram ]
-        fasta: [ meta_ + meta + [ assembly_id: meta_.id ] , fasta_file ]
-    }
+    //
+    // SUBWORKFLOW: Align short reads
+    //
+    ch_cram_to_map = SAMTOOLS_ADDREPLACERG.out.cram
+        .mix ( ch_crams_to_addrg.not_replace_rg )
+        .map{ meta, cram_file -> [ meta + [ reads_size: cram_file.size() ] , cram_file ] }
+        .combine(fasta)
+        .multiMap { meta, cram, meta_, fasta_file ->
+            cram: [ meta_ + meta + [ assembly_id: meta_.id ] , cram ]
+            fasta: [ meta_ + meta + [ assembly_id: meta_.id ] , fasta_file ]
+        }
 
-    CRAM_MAP_ILLUMINA( ch_illumina.fasta, ch_illumina.cram, params.short_aligner, params.short_reads_map_chunk_size )
+    CRAM_MAP_SHORT_READS( ch_cram_to_map.fasta, ch_cram_to_map.cram, params.short_aligner, params.short_reads_map_chunk_size )
     //
     // SUBWORKFLOW: Merge all alignment outputs by specimen
     //
-    MERGE_OUTPUT( CRAM_MAP_ILLUMINA.out.bam )
+    MERGE_OUTPUT( CRAM_MAP_SHORT_READS.out.bam )
 
     emit:
     bam      = MERGE_OUTPUT.out.bam     // channel: [ val(meta), /path/to/bam ]
diff --git a/subworkflows/local/input_check.nf b/subworkflows/local/input_check.nf
index 9a5f2cc3..07be329a 100644
--- a/subworkflows/local/input_check.nf
+++ b/subworkflows/local/input_check.nf
@@ -55,6 +55,7 @@ def create_data_channel ( LinkedHashMap row, datafile, stats ) {
     meta.datatype      = row.datatype
     meta.library       = row.library
     meta.barcode       = row.barcode
+    meta.extra_header  = row.extra_header ? file(row.extra_header, checkExists:true) : []
 
     def platform = (meta.datatype == "hic" || meta.datatype == "illumina") ? "ILLUMINA" :
                 (meta.datatype == "pacbio" || meta.datatype == "pacbio_clr") ? "PACBIO" :

From 0e8e096f0eaa8fe51c88f3fc8625b4ce70bdb7c2 Mon Sep 17 00:00:00 2001
From: sainsachiko <hthhanh.work@gmail.com>
Date: Fri, 29 May 2026 01:22:56 +0100
Subject: [PATCH 04/20] Add PG lines for output alignment files

---
 .../reheader/samtools_replaceheader.nf        | 14 ++++++++---
 subworkflows/local/convert_stats.nf           | 25 +++++++++++++------
 2 files changed, 28 insertions(+), 11 deletions(-)

diff --git a/modules/local/samtools/reheader/samtools_replaceheader.nf b/modules/local/samtools/reheader/samtools_replaceheader.nf
index d522ece5..fd06babd 100644
--- a/modules/local/samtools/reheader/samtools_replaceheader.nf
+++ b/modules/local/samtools/reheader/samtools_replaceheader.nf
@@ -8,8 +8,8 @@ process SAMTOOLS_REHEADER {
         : 'community.wave.seqera.io/library/htslib_samtools:1.23.1--5b6bb4ede7e612e5'}"
 
     input:
-    tuple val(meta), path(file, stageAs: "input/*")
-    path(header)
+    tuple val(meta), path(file, stageAs: "input/*"), path(sample_extra_header, stageAs: "extra_header/*")
+    path(header_template)
 
     output:
     tuple val(meta), path("${prefix}.bam") , optional:true, emit: bam
@@ -22,17 +22,23 @@ process SAMTOOLS_REHEADER {
     script:
     prefix = task.ext.prefix ?: "${meta.id}"
     suffix = file.getExtension()
+    def sq_template = header_template ? " | grep -v ^@SQ && grep '^@SQ' ${header_template}" : ""
+    // Suffix all PG IDs from sample extra_header to keep them distinct from native file-header PG IDs.
+    def pg_extra = sample_extra_header ? "grep '^@PG' ${sample_extra_header} | awk 'BEGIN { FS = OFS = \"\\t\" } { for (i = 1; i <= NF; i++) if (\$i ~ /^ID:/) { \$i = \$i \".extra_header\"; break } print }' || true" : "true"
 
     if ("$file" == "${prefix}.${suffix}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
     """
     # Replace SQ lines with those from external template
-    ( samtools view --no-PG --header-only ${file} | \\
-    grep -v ^@SQ && grep ^@SQ ${header} ) > temp.header.sam
+    ( samtools view --no-PG --header-only ${file} \\
+        ${sq_template} ) > temp.header.sam
 
     # custom sort for readability (retain order of insertion but sort groups by tag)
+    # Add PG lines from sample header
+    # Sort order: HD, SQ, RG, extra PG, PG, other
     ( grep ^@HD temp.header.sam || true && \\
     grep ^@SQ temp.header.sam || true && \\
     grep ^@RG temp.header.sam || true && \\
+    ${pg_extra} && \\
     grep ^@PG temp.header.sam || true && \\
     grep -v -E '^@HD|^@SQ|^@RG|^@PG' temp.header.sam || true; \\
     ) > temp.sorted.header.sam
diff --git a/subworkflows/local/convert_stats.nf b/subworkflows/local/convert_stats.nf
index 27199274..e8ad5005 100644
--- a/subworkflows/local/convert_stats.nf
+++ b/subworkflows/local/convert_stats.nf
@@ -4,9 +4,10 @@
 
 
 // MODULE: local modules
+include { CHANGE_NAME                                   } from '../../modules/local/change_name'
+include { SAMTOOLS_REHEADER as SAMTOOLS_ADD_PG          } from '../../modules/local/samtools/reheader/samtools_replaceheader'
 include { SAMTOOLS_REHEADER as SAMTOOLS_REHEADER_BAM    } from '../../modules/local/samtools/reheader/samtools_replaceheader'
 include { SAMTOOLS_REHEADER as SAMTOOLS_REHEADER_CRAM   } from '../../modules/local/samtools/reheader/samtools_replaceheader'
-include { CHANGE_NAME                                   } from '../../modules/local/change_name'
 
 // MODULE: nf-core modules
 include { BLOBTK_DEPTH                              } from '../../modules/nf-core/blobtk/depth/main'
@@ -34,6 +35,7 @@ workflow CONVERT_STATS {
     // Split outfmt parameter into a list
     def outfmt_options = params.outfmt.split(',').collect { fmt -> fmt.trim() }
 
+
     // (Optionally) Compress the quality scores of Illumina and PacBio CCS alignments
     if ( params.compression == "crumble" ) {
         crumble_selector = bam
@@ -56,7 +58,16 @@ workflow CONVERT_STATS {
     CHANGE_NAME ( ch_bams_for_renaming, fasta )
 
     ch_renamed_bams = CHANGE_NAME.out.file
-    .map { meta, bam_file -> [meta, bam_file, []] }
+    .branch { meta, bam_file ->
+        extra_header: meta.add_pg
+            return [ meta, bam_file, meta.extra_header ]
+        no_extra_header: true
+    }
+
+    SAMTOOLS_ADD_PG( ch_renamed_bams.extra_header, [] )
+    ch_bams_add_pg = SAMTOOLS_ADD_PG.out.bam
+    .mix( ch_renamed_bams.no_extra_header )
+    .map { meta, bam_file -> [ meta, bam_file, [] ] }
 
     // (Optionally) convert to CRAM if it's specified in outfmt
     ch_cram = channel.empty()
@@ -64,12 +75,12 @@ workflow CONVERT_STATS {
 
     fasta_dummy_idx = fasta.map { meta, fasta_file -> [ meta, fasta_file, [] ] }
     if ( "cram" in outfmt_options ) {
-        SAMTOOLS_CRAM ( ch_renamed_bams, fasta_dummy_idx, [[],[]], [[],[]], "" )
+        SAMTOOLS_CRAM ( ch_bams_add_pg, fasta_dummy_idx, [[],[]], [[],[]], "" )
         ch_cram = SAMTOOLS_CRAM.out.cram
         ch_crai = SAMTOOLS_CRAM.out.crai
 
         if ( params.header ) {
-            SAMTOOLS_REHEADER_CRAM ( SAMTOOLS_CRAM.out.cram, header.first() )
+            SAMTOOLS_REHEADER_CRAM ( SAMTOOLS_CRAM.out.cram.map{ meta, cram -> [ meta, cram, []] }, header.first() )
             SAMTOOLS_INDEX_CRAM ( SAMTOOLS_REHEADER_CRAM.out.cram )
             ch_cram = SAMTOOLS_INDEX_CRAM.out.input
             ch_crai = SAMTOOLS_INDEX_CRAM.out.index
@@ -84,8 +95,8 @@ workflow CONVERT_STATS {
     ch_bai = channel.empty()
 
     if ( "bam" in outfmt_options ) {
-        // Reindex BAM
-        ch_bam = params.header ? SAMTOOLS_REHEADER_BAM ( CHANGE_NAME.out.file, header.first() ).bam : CHANGE_NAME.out.file
+        // Re-header && reindex BAM
+        ch_bam = params.header ? SAMTOOLS_REHEADER_BAM ( ch_bams_add_pg, header.first() ).bam : ch_bams_add_pg.map{ meta, bam, _empty-> [ meta, bam ] }
         SAMTOOLS_INDEX_BAM ( ch_bam )
 
         // Set the BAM and BAI channels for emission
@@ -99,7 +110,7 @@ workflow CONVERT_STATS {
     }
 
     // Calculate read depth
-    BLOBTK_DEPTH ( ch_renamed_bams )
+    BLOBTK_DEPTH ( ch_bams_add_pg )
     BGZIP_BEDGRAPH ( BLOBTK_DEPTH.out.bed )
 
     // Calculate statistics

From 3b65a08b57ec4c8da65c2bd137519fc1137933bb Mon Sep 17 00:00:00 2001
From: sainsachiko <hthhanh.work@gmail.com>
Date: Fri, 29 May 2026 02:01:07 +0100
Subject: [PATCH 05/20] Update docs

---
 .nf-core.yml    |  2 +-
 CHANGELOG.md    |  7 +++++++
 CITATION.cff    |  4 ++--
 docs/usage.md   | 13 +++++++------
 nextflow.config |  2 +-
 5 files changed, 18 insertions(+), 10 deletions(-)

diff --git a/.nf-core.yml b/.nf-core.yml
index 177a80fe..0bf7c36f 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -47,4 +47,4 @@ template:
     - igenomes
     - multiqc
     - fastqc
-  version: 2.0.3
+  version: 2.1.0-dev
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 81366e54..349e1ff4 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,13 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+
+## [[v2.1.0-dev](https://github.com/sanger-tol/readmapping/releases/tag/2.1.0-dev)] - 2.1.0-dev - [release-date]
+
+### Enhancements & fixes
+
+- Support extra_header at read-file level to provide `@RG` and `@PG` lines (see [usage](docs/usage.md))
+
 ## [[v2.0.3](https://github.com/sanger-tol/readmapping/releases/tag/2.0.3)] - Hungarian Horntail (patch 3) - [2026-05-15]
 
 ### Enhancements & fixes
diff --git a/CITATION.cff b/CITATION.cff
index bfb43879..265d7c9a 100644
--- a/CITATION.cff
+++ b/CITATION.cff
@@ -57,7 +57,7 @@ license: MIT
 message: If you use this software, please cite it using the metadata from this file
   and all references from CITATIONS.md .
 repository-code: https://github.com/sanger-tol/readmapping
-title: sanger-tol/readmapping v2.0.3 - Hungarian Horntail (patch 3)
+title: sanger-tol/readmapping 2.1.0-dev - 2.1.0-dev
 type: software
 url: https://pipelines.tol.sanger.ac.uk/readmapping
-version: 2.0.3
+version: 2.1.0-dev
diff --git a/docs/usage.md b/docs/usage.md
index 8379b8dc..20ce093c 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -32,12 +32,12 @@ The samplesheet can have as many columns as you desire, however, there is a stri
 A final samplesheet file consisting of both HiC and PacBio data may look something like the one below.
 
 ```console
-specimen,run,datatype,datafile,library,barcode
-specimen1,run1,hic,hic1.cram,,
-specimen1,run2,hic,hic2.cram,,
-specimen2,run3,hic,hic3.cram,,
-specimen2,run4,pacbio,pacbio1.bam,uli,
-specimen3,run5,pacbio,pacbio2.bam,,
+specimen,run,datatype,datafile,library,barcode,extra_header
+specimen1,run1,hic,hic1.cram,,,
+specimen1,run2,hic,hic2.cram,,,
+specimen2,run3,hic,hic3.cram,,,
+specimen2,run4,pacbio,pacbio1.bam,uli,,headers/pacbio_rg.sam
+specimen3,run5,pacbio,pacbio2.bam,,,
 ```
 
 | Column     | Description                                                                                                                                                                                                                                 |
@@ -48,6 +48,7 @@ specimen3,run5,pacbio,pacbio2.bam,,
 | `datafile` | Full path to read data file. Must be `bam`, `cram`, `fastq.gz` or `fq.gz` for `illumina` and `hic`. Must be `bam`, `fastq.gz` or `fq.gz` for `pacbio`, `pacbio_clr`, and `ont`. Note that FASTQ inputs should be interleaved if paired-end. |
 | `library`  | (Optional) The library value is a unique identifier which is assigned to read group (`@RG`) ID. If the library name is not specified, the pipeline will auto-create library name using the data filename provided in the samplesheet.       |
 | `barcode`  | (Optional) Barcode identifier used to trim barcode adapter for PacBio reads. If empty, barcode-specific adapter sequences will not be trimmed.                                                                                              |
+| `extra_header` | (Optional) Path to a SAM file containing additional SAM header lines including `@RG`, `@PG`. These information will be injected into output BAM/CRAM headers. `@RG` lines are overwritten, while `@PG` lines are added to the existing headers (auto add `.extra_header` to `@PG ID`). |
 
 An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline.
 
diff --git a/nextflow.config b/nextflow.config
index f43ad01c..e67c1370 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -322,7 +322,7 @@ manifest {
     mainScript      = 'main.nf'
     defaultBranch   = 'main'
     nextflowVersion = '!>=25.04.0'
-    version         = '2.0.3'
+    version         = '2.1.0-dev'
     doi             = '10.5281/zenodo.6563577'
 }
 

From a89e51a98de0fdd21aa24a34c1aa37443c7ac19c Mon Sep 17 00:00:00 2001
From: sainsachiko <hthhanh.work@gmail.com>
Date: Fri, 29 May 2026 02:13:24 +0100
Subject: [PATCH 06/20] Update tests

---
 assets/samplesheet.csv                    |  16 +-
 assets/samplesheet_long_read.csv          |   8 +-
 assets/samplesheet_short_reads.csv        |   2 +-
 assets/samplesheet_uli.csv                |   6 +-
 tests/default.nf.test                     |  15 +-
 tests/default.nf.test.snap                | 178 +++++++++++++++++++++-
 tests/short_aligner_minimap2.nf.test      |  13 ++
 tests/short_aligner_minimap2.nf.test.snap |  95 +++++++++++-
 tests/uli.nf.test                         |  14 ++
 tests/uli.nf.test.snap                    |  39 ++++-
 tests/uli_no_lima.nf.test                 |  14 ++
 tests/uli_no_lima.nf.test.snap            |  37 ++++-
 tests/untrim.nf.test                      |  14 ++
 tests/untrim.nf.test.snap                 |  71 ++++++++-
 14 files changed, 483 insertions(+), 39 deletions(-)

diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv
index b742ba18..9792153a 100644
--- a/assets/samplesheet.csv
+++ b/assets/samplesheet.csv
@@ -1,8 +1,8 @@
-specimen,run,datatype,datafile,library,barcode
-SAMEA7524438,ERR6688599,illumina,https://tolit.cog.sanger.ac.uk/test-data/Meles_meles/genomic_data/mMelMel1/illumina/31231_3_1.subset.cram,,
-SAMEA7524439,ERR6688600,illumina,https://tolit.cog.sanger.ac.uk/test-data/Meles_meles/genomic_data/mMelMel2/illumina/31231_4_1.subset.fastq.gz,,
-SAMEA7524440,ERR6688402,hic,https://tolit.cog.sanger.ac.uk/test-data/Meles_meles/genomic_data/mMelMel3/hic/35528_2_1.subset.cram,,
-SAMEA7524440,PAE35587,ont,https://tolit.cog.sanger.ac.uk/test-data/Meles_meles/genomic_data/mMelMel3/ont/PAE35587_pass_1f1f0707_115.subset.fastq.gz,,
-SAMEA7524440,PAE35587_test,ont,https://tolit.cog.sanger.ac.uk/test-data/Meles_meles/genomic_data/mMelMel3/ont/PAE35587_pass_1f1f0707_115.subset.addrg.bam,,
-SAMEA7524440,ERR6939248,pacbio,https://tolit.cog.sanger.ac.uk/test-data/Meles_meles/genomic_data/mMelMel3/pacbio/m64094_200910_173211.ccs.bc1022_BAK8B_OA--bc1022_BAK8B_OA.subset.bam,,
-SAMEA7524440,ERR6939249,pacbio,https://tolit.cog.sanger.ac.uk/test-data/Meles_meles/genomic_data/mMelMel3/pacbio/m64094_200911_174739.ccs.bc1022_BAK8B_OA--bc1022_BAK8B_OA.subset.fastq.gz,,bc1022
+specimen,run,datatype,datafile,library,barcode,extra_header
+SAMEA7524438,ERR6688599,illumina,https://tolit.cog.sanger.ac.uk/test-data/Meles_meles/genomic_data/mMelMel1/illumina/31231_3_1.subset.cram,,,
+SAMEA7524439,ERR6688600,illumina,https://tolit.cog.sanger.ac.uk/test-data/Meles_meles/genomic_data/mMelMel2/illumina/31231_4_1.subset.fastq.gz,,,
+SAMEA7524440,ERR6688402,hic,https://tolit.cog.sanger.ac.uk/test-data/Meles_meles/genomic_data/mMelMel3/hic/35528_2_1.subset.cram,,,https://tolit.cog.sanger.ac.uk/test-data/Meles_meles/genomic_data/mMelMel3/hic/35528_2_1.subset.header_no_rg.sam
+SAMEA7524440,PAE35587,ont,https://tolit.cog.sanger.ac.uk/test-data/Meles_meles/genomic_data/mMelMel3/ont/PAE35587_pass_1f1f0707_115.subset.fastq.gz,,,
+SAMEA7524440,PAE35587_test,ont,https://tolit.cog.sanger.ac.uk/test-data/Meles_meles/genomic_data/mMelMel3/ont/PAE35587_pass_1f1f0707_115.subset.addrg.bam,,,
+SAMEA7524440,ERR6939248,pacbio,https://tolit.cog.sanger.ac.uk/test-data/Meles_meles/genomic_data/mMelMel3/pacbio/m64094_200910_173211.ccs.bc1022_BAK8B_OA--bc1022_BAK8B_OA.subset.header_no_rg.bam,,,https://tolit.cog.sanger.ac.uk/test-data/Meles_meles/genomic_data/mMelMel3/pacbio/m64094_200910_173211.ccs.bc1022_BAK8B_OA--bc1022_BAK8B_OA.subset.header.sam
+SAMEA7524440,ERR6939249,pacbio,https://tolit.cog.sanger.ac.uk/test-data/Meles_meles/genomic_data/mMelMel3/pacbio/m64094_200911_174739.ccs.bc1022_BAK8B_OA--bc1022_BAK8B_OA.subset.fastq.gz,,bc1022,https://tolit.cog.sanger.ac.uk/test-data/Meles_meles/genomic_data/mMelMel3/pacbio/m64094_200911_174739.ccs.bc1022_BAK8B_OA--bc1022_BAK8B_OA.subset.header.sam
diff --git a/assets/samplesheet_long_read.csv b/assets/samplesheet_long_read.csv
index 7fbd570a..c3b7831c 100644
--- a/assets/samplesheet_long_read.csv
+++ b/assets/samplesheet_long_read.csv
@@ -1,4 +1,4 @@
-specimen,run,datatype,datafile,library,barcode
-SAMEA7524440,PAE35587,ont,https://tolit.cog.sanger.ac.uk/test-data/Meles_meles/genomic_data/mMelMel3/ont/PAE35587_pass_1f1f0707_115.subset.fastq.gz,,
-SAMEA7524440,ERR6939248,pacbio,https://tolit.cog.sanger.ac.uk/test-data/Meles_meles/genomic_data/mMelMel3/pacbio/m64094_200910_173211.ccs.bc1022_BAK8B_OA--bc1022_BAK8B_OA.subset.bam,,bc1022
-SAMEA7524440,ERR6939249,pacbio,https://tolit.cog.sanger.ac.uk/test-data/Meles_meles/genomic_data/mMelMel3/pacbio/m64094_200911_174739.ccs.bc1022_BAK8B_OA--bc1022_BAK8B_OA.subset.fastq.gz,,bc1022
+specimen,run,datatype,datafile,library,barcode,extra_header
+SAMEA7524440,PAE35587,ont,https://tolit.cog.sanger.ac.uk/test-data/Meles_meles/genomic_data/mMelMel3/ont/PAE35587_pass_1f1f0707_115.subset.fastq.gz,,,
+SAMEA7524440,ERR6939248,pacbio,https://tolit.cog.sanger.ac.uk/test-data/Meles_meles/genomic_data/mMelMel3/pacbio/m64094_200910_173211.ccs.bc1022_BAK8B_OA--bc1022_BAK8B_OA.subset.bam,,bc1022,
+SAMEA7524440,ERR6939249,pacbio,https://tolit.cog.sanger.ac.uk/test-data/Meles_meles/genomic_data/mMelMel3/pacbio/m64094_200911_174739.ccs.bc1022_BAK8B_OA--bc1022_BAK8B_OA.subset.fastq.gz,,bc1022,https://tolit.cog.sanger.ac.uk/test-data/Meles_meles/genomic_data/mMelMel3/pacbio/m64094_200911_174739.ccs.bc1022_BAK8B_OA--bc1022_BAK8B_OA.subset.header.sam
diff --git a/assets/samplesheet_short_reads.csv b/assets/samplesheet_short_reads.csv
index b7865466..9af9dc64 100644
--- a/assets/samplesheet_short_reads.csv
+++ b/assets/samplesheet_short_reads.csv
@@ -1,4 +1,4 @@
 specimen,run,datatype,datafile,library,barcode
 SAMEA7524438,ERR6688599,illumina,https://tolit.cog.sanger.ac.uk/test-data/Meles_meles/genomic_data/mMelMel1/illumina/31231_3_1.subset.bam,,
 SAMEA7524439,ERR6688600,illumina,https://tolit.cog.sanger.ac.uk/test-data/Meles_meles/genomic_data/mMelMel2/illumina/31231_4_1.subset.fastq.gz,,
-SAMEA7524440,ERR6688402,hic,https://tolit.cog.sanger.ac.uk/test-data/Meles_meles/genomic_data/mMelMel3/hic/35528_2_1.subset.cram,,
+SAMEA7524440,ERR6688402,hic,https://tolit.cog.sanger.ac.uk/test-data/Meles_meles/genomic_data/mMelMel3/hic/35528_2_1.subset.cram,,,https://tolit.cog.sanger.ac.uk/test-data/Meles_meles/genomic_data/mMelMel3/hic/35528_2_1.subset.header_no_rg.sam
diff --git a/assets/samplesheet_uli.csv b/assets/samplesheet_uli.csv
index 793b6fe7..16ac2758 100644
--- a/assets/samplesheet_uli.csv
+++ b/assets/samplesheet_uli.csv
@@ -1,3 +1,3 @@
-specimen,run,datatype,datafile,library,barcode
-SAMEA114784749,ERR14209104,pacbio,https://tolit.cog.sanger.ac.uk/test-data/Acropora_cervicornis/genomic_data/m84093_241116_151316_s2.hifi_reads.bc2028.subset.bam,uli,bc2028
-SAMEA114784749,ERR14209104_test,pacbio,https://tolit.cog.sanger.ac.uk/test-data/Acropora_cervicornis/genomic_data/m84093_241116_151316_s2.hifi_reads.bc2028.subset.bam,,bc2028
+specimen,run,datatype,datafile,library,barcode,extra_header
+SAMEA114784749,ERR14209104,pacbio,https://tolit.cog.sanger.ac.uk/test-data/Acropora_cervicornis/genomic_data/m84093_241116_151316_s2.hifi_reads.bc2028.subset.bam,uli,bc2028,
+SAMEA114784749,ERR14209104_test,pacbio,https://tolit.cog.sanger.ac.uk/test-data/Acropora_cervicornis/genomic_data/m84093_241116_151316_s2.hifi_reads.bc2028.subset.bam,,bc2028,
diff --git a/tests/default.nf.test b/tests/default.nf.test
index a2806c11..e827d4a4 100644
--- a/tests/default.nf.test
+++ b/tests/default.nf.test
@@ -27,6 +27,17 @@ nextflow_pipeline {
             def bam_path = getAllFilesFromDir(params.outdir, include: ['**/*.bam'], relative: true, includeDir: false)
             def fasta = 'https://tolit.cog.sanger.ac.uk/test-data/Meles_meles/assembly/release/mMelMel3.1_paternal_haplotype/GCA_922984935.2.subset.fasta'
 
+            def strip_absolute_path_lines = { text ->
+                def lines = text?.getClass()?.isArray()
+                    ? text.toList()
+                    : (text instanceof Collection ? text : (text?.toString()?.readLines() ?: []))
+                lines
+                    .collect { line ->
+                        line.toString()
+                            .replaceAll(/\bUR:\/((?:[^\/\s]+\/){2})\S+/, 'UR:/$1<ABS_PATH>')
+                    }
+            }
+
             assertAll(
                 { assert workflow.success},
                 { assert snapshot(
@@ -40,8 +51,10 @@ nextflow_pipeline {
                     // Stable mapping files
                     bam_path.collect{ f -> [(new File(f).getName()): bam("${params.outdir}/${f}").getStatistics()] }.collectEntries{ it }.sort(),
                     cram_path.collect{ f -> [(new File(f).getName()): cram("${params.outdir}/${f}", fasta).getStatistics()] }.collectEntries{ it }.sort(),
+                    bam_path.collect{ f -> [(new File(f).getName()): strip_absolute_path_lines(bam("${params.outdir}/${f}").getHeader())] }.collectEntries{ it }.sort(),
+                    cram_path.collect{ f -> [(new File(f).getName()): strip_absolute_path_lines(cram("${params.outdir}/${f}", fasta).getHeader())] }.collectEntries{ it }.sort(),
 
-                     // Stable trimming json
+                    // Stable trimming json
                     hifitrimmer_json.collect{ f ->
                         def obj = path("${params.outdir}/${f}").json
                         obj.remove('run_info')
diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap
index 8dec181a..d33de6ed 100644
--- a/tests/default.nf.test.snap
+++ b/tests/default.nf.test.snap
@@ -1,7 +1,7 @@
 {
     "-profile test": {
         "content": [
-            175,
+            182,
             {
                 "BGZIP_BEDGRAPH": {
                     "samtools": "1.23.1"
@@ -73,6 +73,9 @@
                 "SAMTOOLS_ADDREPLACERG": {
                     "samtools": "1.23.1"
                 },
+                "SAMTOOLS_ADD_PG": {
+                    "samtools": "1.23.1"
+                },
                 "SAMTOOLS_CRAM": {
                     "samtools": "1.23.1"
                 },
@@ -110,7 +113,7 @@
                     "samtools": "1.23.1"
                 },
                 "Workflow": {
-                    "sanger-tol/readmapping": "v2.0.3"
+                    "sanger-tol/readmapping": "v2.1.0-dev"
                 }
             },
             [
@@ -377,6 +380,175 @@
                     "sorted": false
                 }
             },
+            {
+                
+            },
+            {
+                "GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.bwamem2.cram": [
+                    "@HD\tVN:1.6\tSO:coordinate",
+                    "@SQ\tSN:OV277441.1\tLN:7999920\tM5:0457acf8690429f1c98ee545cb8573b8\tUR:/nfs/treeoflife-01/<ABS_PATH>\tAS:GCA_922984935.2\tAN:SUPER_1\tSP:Meles meles",
+                    "@RG\tID:35528_2_1\tPL:ILLUMINA\tSM:SAMEA7524440",
+                    "@PG\tID:SCS.extra_header\tVN:1.7.0\tPN:NovaSeq Control Software\tDS:Controlling software on instrument",
+                    "@PG\tID:basecalling.extra_header\tPP:SCS\tVN:Unknown\tPN:Unknown\tDS:Basecalling Package",
+                    "@PG\tID:bambi.extra_header\tPP:basecalling\tVN:0.13.1\tCL:/software/pkgg/bambi/0.13.1/bin/bambi i2b --intensity-dir=/lustre/scratch121/esa-sv-20200210-01/IL_seq_data/analysis/201117_A00948_0206_AHGML2DSXY/Data/Intensities --basecalls-dir=/lustre/scratch121/esa-sv-20200210-01/IL_seq_data/analysis/201117_A00948_0206_AHGML2DSXY/Data/Intensities/BaseCalls --lane=2 --platform-unit=201117_A00948_0206_AHGML2DSXY_2 --read-group-id=35528_2 --study-name=\"ERP116890: Sequencing and assembly of genomes from British species for the Darwin Tree of Life Project. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ \" --sample-alias=SAMEA5962964,mCerEla1 --threads=8 --output-file=- --compression-level=0\tPN:bambi\tDS:Convert Illumina BCL to BAM or SAM file",
+                    "@PG\tID:bambi.1.extra_header\tPN:bambi\tPP:bambi\tVN:0.13.1\tCL:/software/pkgg/bambi/0.13.1/bin/bambi decode --metrics-file /lustre/scratch121/esa-sv-20200210-01/IL_seq_data/analysis/201117_A00948_0206_AHGML2DSXY/Data/Intensities/BAM_basecalls_20201119-090808/35528_2.bam.tag_decode.metrics --barcode-file /lustre/scratch121/esa-sv-20200210-01/IL_seq_data/analysis/201117_A00948_0206_AHGML2DSXY/Data/Intensities/BAM_basecalls_20201119-090808/metadata_cache_35528/lane_2.taglist --compression-level 0 -",
+                    "@PG\tID:bamcollate2.extra_header\tPN:bamcollate2\tCL:/software/pkgg/biobambam2/2.0.79/bin/bamcollate2 collate=2 level=0\tPP:bambi.1\tVN:2.0.79",
+                    "@PG\tID:minimap2.extra_header\tPN:minimap2\tCL:minimap2 -ax sr --MD -t 3 -Y -F 1200 -K 100000000 /lustre/scratch121/npg_repository/references/PhiX/Sanger-SNPs/all/minimap2/phix_unsnipped_short_no_N.fa.mmi /tmp/wr_cwd/0/e/8/dce75fe12433429e1b439b8872bc7693328371/tmp/s0uOqe6xfG/alnphix_bamtofastq_out\tPP:bamcollate2\tVN:2.10-r761",
+                    "@PG\tID:samtools.extra_header\tPN:samtools\tCL:/software/pkgg/samtools/1.11.0/bin/samtools view --threads 3 -u -F 0x900 -\tPP:minimap2\tVN:1.11",
+                    "@PG\tID:bam12auxmerge.extra_header\tPN:bam12auxmerge\tCL:/software/pkgg/biobambam2/2.0.79/bin/bam12auxmerge level=0 rankstrip=1 ranksplit=1 zztoname=0 clipreinsert=1 /tmp/wr_cwd/0/e/8/dce75fe12433429e1b439b8872bc7693328371/tmp/ac_8ARdDJl/tee_collated:td1_out\tPP:samtools\tVN:2.0.79",
+                    "@PG\tID:samtools.1.extra_header\tPN:samtools\tPP:bam12auxmerge\tVN:1.11\tCL:/software/pkgg/samtools/1.11.0/bin/samtools split --threads 4 --output-fmt cram,no_ref=1 -f /lustre/scratch121/esa-sv-20200210-01/IL_seq_data/analysis/201117_A00948_0206_AHGML2DSXY/Data/Intensities/BAM_basecalls_20201119-090808/no_cal/%!.cram -",
+                    "@PG\tID:samtools.2.extra_header\tPN:samtools\tPP:samtools.1\tVN:1.11\tCL:/software/pkgg/samtools/1.11.0/bin/samtools merge -n -O BAM -l 0 --input-fmt-option no_ref=1 - /lustre/scratch121/esa-sv-20200210-01/IL_seq_data/analysis/201117_A00948_0206_AHGML2DSXY/Data/Intensities/BAM_basecalls_20201119-090808/no_cal/35528_2#1.cram",
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+                    "@PG\tID:bambi.2.extra_header\tPN:bambi\tPP:spf\tVN:0.13.1\tCL:/software/pkgg/bambi/0.13.1/bin/bambi select --compression-level 0 --input /tmp/wr_cwd/5/0/6/86a8369ba62bab2227fd63e2ff1ad119662395/tmp/9RE_mnwwls/ssfqc_tee_ssfqc:straight_through1_out --output /tmp/wr_cwd/5/0/6/86a8369ba62bab2227fd63e2ff1ad119662395/tmp/b6x1p8j3v_/alignment_filter:phix_bam_out_out -n /tmp/wr_cwd/5/0/6/86a8369ba62bab2227fd63e2ff1ad119662395/tmp/IuuBniSlRB/alignment_filter:target_bam_out_out -m 35528_2#1_bam_alignment_filter_metrics.json\tDS:Split alignments into different files",
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+                    "@PG\tID:bwa-mem2\tPN:bwa-mem2\tVN:2.2.1\tCL:bwa-mem2 mem -5SPCp -t 4 ./bwamem2/GCA_922984935.2.subset.unmasked.fa -C -H @RG\\tID:35528_2_1\\tPL:ILLUMINA\\tSM:SAMEA7524440 -",
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+                    "@PG\tID:samtools.3\tPN:samtools\tPP:samtools.2\tVN:1.23.1\tCL:samtools merge --threads 3 -c -p --reference GCA_922984935.2.subset.unmasked.fa - 1/35528_2_1.subset_addRG.cram.0.SAMEA7524440.ERR6688402.bam 2/35528_2_1.subset_addRG.cram.1.SAMEA7524440.ERR6688402.bam",
+                    "@PG\tID:samtools.4\tPN:samtools\tPP:samtools.3\tVN:1.23.1\tCL:samtools markdup -T SAMEA7524440.ERR6688402 -f SAMEA7524440.ERR6688402.metrics --threads 4 --reference GCA_922984935.2.subset.unmasked.fa - SAMEA7524440.ERR6688402.bam",
+                    "@PG\tID:crumble\tPN:crumble\tPP:samtools.4\tVN:0.9.1\tCL:crumble -O bam SAMEA7524440.ERR6688402.bam SAMEA7524440.ERR6688402.crumble.bam",
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+                    "@PG\tID:samtools.13\tPN:samtools\tPP:samtools.7\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1,lossy_names=1 --write-index -o GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.bwamem2.cram GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.bwamem2.bam",
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+                    "@PG\tID:samtools.21\tPN:samtools\tPP:samtools.15\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.bwamem2.cram",
+                    "@PG\tID:samtools.22\tPN:samtools\tPP:samtools.16\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.bwamem2.cram"
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+                    "@RG\tID:31231_3#1\tDT:2019-10-03T01:00:00+0100\tPU:191003_HX4_31231_A_H3353CCX2_3#1\tLB:23687379\tPG:SCS\tSM:SAMEA5962962\tCN:SC\tPL:ILLUMINA\tDS:ERP114452: Sequencing and assembly of vertebrate genomes from British species for the Darwin Tree of Life Project in collaboration with the Vertebrate Genomes Project. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",
+                    "@PG\tID:bwa-mem2\tPN:bwa-mem2\tVN:2.2.1\tCL:bwa-mem2 mem -p -t 4 ./bwamem2/GCA_922984935.2.subset.unmasked.fa -C -H @RG\\tID:31231_3#1\\tDT:2019-10-03T00:00:00+0000\\tPU:191003_HX4_31231_A_H3353CCX2_3#1\\tLB:23687379\\tPG:SCS\\tSM:SAMEA5962962\\tCN:SC\\tPL:ILLUMINA\\tDS:ERP114452: Sequencing and assembly of vertebrate genomes from British species for the Darwin Tree of Life Project in collaboration with the Vertebrate Genomes Project. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ -",
+                    "@PG\tID:samtools\tPN:samtools\tPP:bwa-mem2\tVN:1.22.1\tCL:samtools fixmate -mpu - -",
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+                    "@PG\tID:samtools.3\tPN:samtools\tPP:samtools.2\tVN:1.23.1\tCL:samtools merge --threads 3 -c -p --reference GCA_922984935.2.subset.unmasked.fa - 1/31231_3_1.subset.cram.0.SAMEA7524438.ERR6688599.bam 2/31231_3_1.subset.cram.1.SAMEA7524438.ERR6688599.bam",
+                    "@PG\tID:samtools.4\tPN:samtools\tPP:samtools.3\tVN:1.23.1\tCL:samtools markdup -T SAMEA7524438.ERR6688599 -f SAMEA7524438.ERR6688599.metrics --threads 4 --reference GCA_922984935.2.subset.unmasked.fa - SAMEA7524438.ERR6688599.bam",
+                    "@PG\tID:crumble\tPN:crumble\tPP:samtools.4\tVN:0.9.1\tCL:crumble -O bam SAMEA7524438.ERR6688599.bam SAMEA7524438.ERR6688599.crumble.bam",
+                    "@PG\tID:samtools.5\tPN:samtools\tPP:crumble\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1,lossy_names=1 --write-index -o GCA_922984935.2.subset.illumina.SAMEA7524438.ERR6688599.bwamem2.cram GCA_922984935.2.subset.illumina.SAMEA7524438.ERR6688599.bwamem2.bam",
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+                    "@PG\tID:samtools.3\tPN:samtools\tPP:samtools.2\tVN:1.23.1\tCL:samtools merge --threads 3 -c -p --reference GCA_922984935.2.subset.unmasked.fa - 1/SAMEA7524439.ERR6688600_addRG.cram.0.SAMEA7524439.ERR6688600.bam 2/SAMEA7524439.ERR6688600_addRG.cram.1.SAMEA7524439.ERR6688600.bam",
+                    "@PG\tID:samtools.4\tPN:samtools\tPP:samtools.3\tVN:1.23.1\tCL:samtools markdup -T SAMEA7524439.ERR6688600 -f SAMEA7524439.ERR6688600.metrics --threads 4 --reference GCA_922984935.2.subset.unmasked.fa - SAMEA7524439.ERR6688600.bam",
+                    "@PG\tID:crumble\tPN:crumble\tPP:samtools.4\tVN:0.9.1\tCL:crumble -O bam SAMEA7524439.ERR6688600.bam SAMEA7524439.ERR6688600.crumble.bam",
+                    "@PG\tID:samtools.5\tPN:samtools\tPP:crumble\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1,lossy_names=1 --write-index -o GCA_922984935.2.subset.illumina.SAMEA7524439.ERR6688600.bwamem2.cram GCA_922984935.2.subset.illumina.SAMEA7524439.ERR6688600.bwamem2.bam",
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+                    "@PG\tID:samtools.2\tPN:samtools\tPP:samtools.1\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1 --write-index -o GCA_922984935.2.subset.ont.SAMEA7524440.PAE35587.minimap2.cram GCA_922984935.2.subset.ont.SAMEA7524440.PAE35587.minimap2.bam",
+                    "@PG\tID:samtools.3\tPN:samtools\tPP:samtools.2\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.ont.SAMEA7524440.PAE35587.minimap2.cram"
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+                    "@RG\tID:PAE35587_pass_1f1f0707_115\tPL:ONT\tSM:mMelMel3",
+                    "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t4 -ax map-ont -y -R @RG\\tID:PAE35587_pass_1f1f0707_115\\tPL:ONT\\tSM:mMelMel3 -I1G -a GCA_922984935.2.subset.unmasked.mmi -",
+                    "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.23.1\tCL:samtools sort -@ 3 -o SAMEA7524440.PAE35587_test_other.fastq.gz.0.SAMEA7524440.PAE35587_test.bam -T SAMEA7524440.PAE35587_test_other.fastq.gz.0.SAMEA7524440.PAE35587_test_sort_tmp --write-index -l1 -",
+                    "@PG\tID:samtools.1\tPN:samtools\tPP:samtools\tVN:1.23.1\tCL:samtools merge --threads 3 -c -p --reference GCA_922984935.2.subset.unmasked.fa SAMEA7524440.PAE35587_test.merge.bam 1/SAMEA7524440.PAE35587_test_other.fastq.gz.0.SAMEA7524440.PAE35587_test.bam",
+                    "@PG\tID:samtools.2\tPN:samtools\tPP:samtools.1\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1 --write-index -o GCA_922984935.2.subset.ont.SAMEA7524440.PAE35587_test.minimap2.cram GCA_922984935.2.subset.ont.SAMEA7524440.PAE35587_test.minimap2.bam",
+                    "@PG\tID:samtools.3\tPN:samtools\tPP:samtools.2\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.ont.SAMEA7524440.PAE35587_test.minimap2.cram"
+                ],
+                "GCA_922984935.2.subset.ont.SAMEA7524440.merged_1.minimap2.cram": [
+                    "@HD\tVN:1.6\tSO:coordinate",
+                    "@SQ\tSN:OV277441.1\tLN:7999920\tM5:0457acf8690429f1c98ee545cb8573b8\tUR:/nfs/treeoflife-01/<ABS_PATH>\tAS:GCA_922984935.2\tAN:SUPER_1\tSP:Meles meles",
+                    "@RG\tID:PAE35587_pass_1f1f0707_115\tPL:ONT\tSM:mMelMel3",
+                    "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t4 -ax map-ont -y -R @RG\\tID:PAE35587_pass_1f1f0707_115\\tPL:ONT\\tSM:mMelMel3 -I1G -a GCA_922984935.2.subset.unmasked.mmi -",
+                    "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.23.1\tCL:samtools sort -@ 3 -o SAMEA7524440.PAE35587_test_other.fastq.gz.0.SAMEA7524440.PAE35587_test.bam -T SAMEA7524440.PAE35587_test_other.fastq.gz.0.SAMEA7524440.PAE35587_test_sort_tmp --write-index -l1 -",
+                    "@PG\tID:samtools.1\tPN:samtools\tPP:samtools\tVN:1.23.1\tCL:samtools merge --threads 3 -c -p --reference GCA_922984935.2.subset.unmasked.fa SAMEA7524440.PAE35587_test.merge.bam 1/SAMEA7524440.PAE35587_test_other.fastq.gz.0.SAMEA7524440.PAE35587_test.bam",
+                    "@PG\tID:samtools.2\tPN:samtools\tPP:samtools.1\tVN:1.23.1\tCL:samtools merge --threads 3 -c -p SAMEA7524440.merged_1.merge.bam 1/SAMEA7524440.PAE35587_test.merge.bam 2/SAMEA7524440.PAE35587.merge.bam",
+                    "@PG\tID:samtools.3\tPN:samtools\tPP:samtools.2\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1 --write-index -o GCA_922984935.2.subset.ont.SAMEA7524440.merged_1.minimap2.cram GCA_922984935.2.subset.ont.SAMEA7524440.merged_1.minimap2.bam",
+                    "@PG\tID:samtools.4\tPN:samtools\tPP:samtools.3\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.ont.SAMEA7524440.merged_1.minimap2.cram"
+                ],
+                "GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939248.minimap2.cram": [
+                    "@HD\tVN:1.6\tSO:coordinate",
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+                    "@RG\tID:61ddc6c3/15--15\tPL:PACBIO\tDS:READTYPE=CCS;BINDINGKIT=101-789-500;SEQUENCINGKIT=101-826-100;BASECALLERVERSION=5.0.0;FRAMERATEHZ=100.000000;BarcodeFile=/lustre/scratch116/vr/projects/vgp/ref/barcodes/Sequel_16_Barcodes_v3.fasta;BarcodeHash=e418d89cefcbef90f3cb0e6455b7e2a3;BarcodeCount=16;BarcodeMode=Symmetric;BarcodeQuality=Score\tLB:DN615654G-A1\tPU:m64094_200910_173211\tPM:SEQUELII\tBC:CACTCACGTGTGATATT\tCM:S/P4-C2/5.0-8M\tSM:SAMEA7524440",
+                    "@PG\tID:ccs-4.2.0.extra_header\tPN:ccs\tVN:4.2.0\tDS:Generate circular consensus sequences (ccs) from subreads.\tCL:ccs ccs --chunk 1/64 -j 8 --max-length 50000 ../../m64094_200910_173211.subreads.bam m64094_200910_173211.ccs.bam",
+                    "@PG\tID:lima.extra_header\tVN:1.11.0 (commit v1.11.0)\tCL:lima -j 8 --split-bam-named --same --peek-guess --guess-min-count 1000 --ccs m64094_200910_173211.ccs.bam /lustre/scratch116/vr/projects/vgp/ref/barcodes/Sequel_16_Barcodes_v3.fasta lima/m64094_200910_173211.ccs.bam",
+                    "@PG\tID:samtools.extra_header\tPN:samtools\tVN:1.10\tPP:ccs-4.2.0\tCL:samtools merge -@8 -ncp -b m64094_200910_173211.chunks.fofn m64094_200910_173211.ccs.bam",
+                    "@PG\tID:samtools.1.extra_header\tPN:samtools\tPP:samtools\tVN:1.19.2\tCL:samtools view -b -h -N /nfs/users/nfs_m/mm49/READS -o /nfs/users/nfs_m/mm49/x.bam m64094_200910_173211.ccs.bc1022_BAK8B_OA--bc1022_BAK8B_OA.bam",
+                    "@PG\tID:samtools.2.extra_header\tPN:samtools\tPP:samtools.1\tVN:1.23.1\tCL:samtools view -H m64094_200910_173211.ccs.bc1022_BAK8B_OA--bc1022_BAK8B_OA.subset.bam",
+                    "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t4 -ax map-hifi --cs=short -y -R @RG\\tID:61ddc6c3/15--15\\tPL:PACBIO\\tDS:READTYPE=CCS;BINDINGKIT=101-789-500;SEQUENCINGKIT=101-826-100;BASECALLERVERSION=5.0.0;FRAMERATEHZ=100.000000;BarcodeFile=/lustre/scratch116/vr/projects/vgp/ref/barcodes/Sequel_16_Barcodes_v3.fasta;BarcodeHash=e418d89cefcbef90f3cb0e6455b7e2a3;BarcodeCount=16;BarcodeMode=Symmetric;BarcodeQuality=Score\\tLB:DN615654G-A1\\tPU:m64094_200910_173211\\tPM:SEQUELII\\tBC:CACTCACGTGTGATATT\\tCM:S/P4-C2/5.0-8M\\tSM:SAMEA7524440 -I1G -a GCA_922984935.2.subset.unmasked.mmi -",
+                    "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.23.1\tCL:samtools sort -@ 3 -o pacbio.SAMEA7524440.ERR6939248.hifitrimmer.fastq.gz.0.SAMEA7524440.ERR6939248.bam -T pacbio.SAMEA7524440.ERR6939248.hifitrimmer.fastq.gz.0.SAMEA7524440.ERR6939248_sort_tmp --write-index -l1 -",
+                    "@PG\tID:samtools.1\tPN:samtools\tPP:samtools\tVN:1.23.1\tCL:samtools merge --threads 3 -c -p --reference GCA_922984935.2.subset.unmasked.fa SAMEA7524440.ERR6939248.merge.bam 1/pacbio.SAMEA7524440.ERR6939248.hifitrimmer.fastq.gz.0.SAMEA7524440.ERR6939248.bam",
+                    "@PG\tID:crumble\tPN:crumble\tPP:samtools.1\tVN:0.9.1\tCL:crumble -y pbccs -O bam SAMEA7524440.ERR6939248.merge.bam SAMEA7524440.ERR6939248.merge.crumble.bam",
+                    "@PG\tID:samtools.2\tPN:samtools\tPP:samtools.1.extra_header\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939248.minimap2.bam",
+                    "@PG\tID:samtools.3\tPN:samtools\tPP:samtools.2.extra_header\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939248.minimap2.bam",
+                    "@PG\tID:samtools.4\tPN:samtools\tPP:crumble\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939248.minimap2.bam",
+                    "@PG\tID:samtools.5\tPN:samtools\tPP:samtools.2\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1 --write-index -o GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939248.minimap2.cram GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939248.minimap2.bam",
+                    "@PG\tID:samtools.6\tPN:samtools\tPP:samtools.3\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1 --write-index -o GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939248.minimap2.cram GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939248.minimap2.bam",
+                    "@PG\tID:samtools.7\tPN:samtools\tPP:samtools.4\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1 --write-index -o GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939248.minimap2.cram GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939248.minimap2.bam",
+                    "@PG\tID:samtools.8\tPN:samtools\tPP:samtools.5\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939248.minimap2.cram",
+                    "@PG\tID:samtools.9\tPN:samtools\tPP:samtools.6\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939248.minimap2.cram",
+                    "@PG\tID:samtools.10\tPN:samtools\tPP:samtools.7\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939248.minimap2.cram"
+                ],
+                "GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.cram": [
+                    "@HD\tVN:1.6\tSO:coordinate",
+                    "@SQ\tSN:OV277441.1\tLN:7999920\tM5:0457acf8690429f1c98ee545cb8573b8\tUR:/nfs/treeoflife-01/<ABS_PATH>\tAS:GCA_922984935.2\tAN:SUPER_1\tSP:Meles meles",
+                    "@RG\tID:m64094_200911_174739\tPL:PACBIO\tSM:SAMEA7524440",
+                    "@PG\tID:samtools.extra_header\tPN:samtools\tVN:1.22.1\tCL:samtools collate --output-fmt cram -O -u -T mMelMel3_T4.collate --threads 4 --reference GCA_922984935.2.subset.unmasked.fasta m64094_200911_174739.ccs.bc1022_BAK8B_OA--bc1022_BAK8B_OA.subset.fastq.gz -",
+                    "@PG\tID:samtools.1.extra_header\tPN:samtools\tPP:samtools\tVN:1.22.1\tCL:samtools fixmate -m -u --threads 4 - -",
+                    "@PG\tID:samtools.2.extra_header\tPN:samtools\tPP:samtools.1\tVN:1.22.1\tCL:samtools sort -u -T mMelMel3_T4.sort --threads 4 -",
+                    "@PG\tID:samtools.3.extra_header\tPN:samtools\tPP:samtools.2\tVN:1.22.1\tCL:samtools markdup -T mMelMel3_T4.markdup -f mMelMel3_T4.metrics --threads 4 - mMelMel3_T4.cram",
+                    "@PG\tID:samtools.4.extra_header\tPN:samtools\tPP:samtools.3\tVN:1.23.1\tCL:samtools view -H m64094_200911_174739.ccs.bc1022_BAK8B_OA--bc1022_BAK8B_OA.subset.cram",
+                    "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t4 -ax map-hifi --cs=short -y -R @RG\\tID:m64094_200911_174739\\tPL:PACBIO\\tSM:SAMEA7524440 -I1G -a GCA_922984935.2.subset.unmasked.mmi -",
+                    "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.23.1\tCL:samtools sort -@ 3 -o pacbio.SAMEA7524440.ERR6939249.hifitrimmer.fastq.gz.0.SAMEA7524440.ERR6939249.bam -T pacbio.SAMEA7524440.ERR6939249.hifitrimmer.fastq.gz.0.SAMEA7524440.ERR6939249_sort_tmp --write-index -l1 -",
+                    "@PG\tID:samtools.1\tPN:samtools\tPP:samtools\tVN:1.23.1\tCL:samtools merge --threads 3 -c -p --reference GCA_922984935.2.subset.unmasked.fa SAMEA7524440.ERR6939249.merge.bam 1/pacbio.SAMEA7524440.ERR6939249.hifitrimmer.fastq.gz.0.SAMEA7524440.ERR6939249.bam",
+                    "@PG\tID:crumble\tPN:crumble\tPP:samtools.1\tVN:0.9.1\tCL:crumble -y pbccs -O bam SAMEA7524440.ERR6939249.merge.bam SAMEA7524440.ERR6939249.merge.crumble.bam",
+                    "@PG\tID:samtools.2\tPN:samtools\tPP:samtools.1.extra_header\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.bam",
+                    "@PG\tID:samtools.3\tPN:samtools\tPP:samtools.2.extra_header\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.bam",
+                    "@PG\tID:samtools.4\tPN:samtools\tPP:crumble\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.bam",
+                    "@PG\tID:samtools.5\tPN:samtools\tPP:samtools.3.extra_header\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1 --write-index -o GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.cram GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.bam",
+                    "@PG\tID:samtools.6\tPN:samtools\tPP:samtools.4.extra_header\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1 --write-index -o GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.cram GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.bam",
+                    "@PG\tID:samtools.7\tPN:samtools\tPP:samtools.4\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1 --write-index -o GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.cram GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.bam",
+                    "@PG\tID:samtools.8\tPN:samtools\tPP:samtools.5\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.cram",
+                    "@PG\tID:samtools.9\tPN:samtools\tPP:samtools.6\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.cram",
+                    "@PG\tID:samtools.10\tPN:samtools\tPP:samtools.7\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.cram"
+                ],
+                "GCA_922984935.2.subset.pacbio.SAMEA7524440.merged_1.minimap2.cram": [
+                    "@HD\tVN:1.6\tSO:coordinate",
+                    "@SQ\tSN:OV277441.1\tLN:7999920\tM5:0457acf8690429f1c98ee545cb8573b8\tUR:/nfs/treeoflife-01/<ABS_PATH>\tAS:GCA_922984935.2\tAN:SUPER_1\tSP:Meles meles",
+                    "@RG\tID:61ddc6c3/15--15\tPL:PACBIO\tDS:READTYPE=CCS;BINDINGKIT=101-789-500;SEQUENCINGKIT=101-826-100;BASECALLERVERSION=5.0.0;FRAMERATEHZ=100.000000;BarcodeFile=/lustre/scratch116/vr/projects/vgp/ref/barcodes/Sequel_16_Barcodes_v3.fasta;BarcodeHash=e418d89cefcbef90f3cb0e6455b7e2a3;BarcodeCount=16;BarcodeMode=Symmetric;BarcodeQuality=Score\tLB:DN615654G-A1\tPU:m64094_200910_173211\tPM:SEQUELII\tBC:CACTCACGTGTGATATT\tCM:S/P4-C2/5.0-8M\tSM:SAMEA7524440",
+                    "@RG\tID:m64094_200911_174739\tPL:PACBIO\tSM:SAMEA7524440",
+                    "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t4 -ax map-hifi --cs=short -y -R @RG\\tID:61ddc6c3/15--15\\tPL:PACBIO\\tDS:READTYPE=CCS;BINDINGKIT=101-789-500;SEQUENCINGKIT=101-826-100;BASECALLERVERSION=5.0.0;FRAMERATEHZ=100.000000;BarcodeFile=/lustre/scratch116/vr/projects/vgp/ref/barcodes/Sequel_16_Barcodes_v3.fasta;BarcodeHash=e418d89cefcbef90f3cb0e6455b7e2a3;BarcodeCount=16;BarcodeMode=Symmetric;BarcodeQuality=Score\\tLB:DN615654G-A1\\tPU:m64094_200910_173211\\tPM:SEQUELII\\tBC:CACTCACGTGTGATATT\\tCM:S/P4-C2/5.0-8M\\tSM:SAMEA7524440 -I1G -a GCA_922984935.2.subset.unmasked.mmi -",
+                    "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.23.1\tCL:samtools sort -@ 3 -o pacbio.SAMEA7524440.ERR6939248.hifitrimmer.fastq.gz.0.SAMEA7524440.ERR6939248.bam -T pacbio.SAMEA7524440.ERR6939248.hifitrimmer.fastq.gz.0.SAMEA7524440.ERR6939248_sort_tmp --write-index -l1 -",
+                    "@PG\tID:samtools.1\tPN:samtools\tPP:samtools\tVN:1.23.1\tCL:samtools merge --threads 3 -c -p --reference GCA_922984935.2.subset.unmasked.fa SAMEA7524440.ERR6939248.merge.bam 1/pacbio.SAMEA7524440.ERR6939248.hifitrimmer.fastq.gz.0.SAMEA7524440.ERR6939248.bam",
+                    "@PG\tID:samtools.2\tPN:samtools\tPP:samtools.1\tVN:1.23.1\tCL:samtools merge --threads 3 -c -p SAMEA7524440.merged_1.merge.bam 1/SAMEA7524440.ERR6939248.merge.bam 2/SAMEA7524440.ERR6939249.merge.bam",
+                    "@PG\tID:crumble\tPN:crumble\tPP:samtools.2\tVN:0.9.1\tCL:crumble -y pbccs -O bam SAMEA7524440.merged_1.merge.bam SAMEA7524440.merged_1.merge.crumble.bam",
+                    "@PG\tID:samtools.3\tPN:samtools\tPP:crumble\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1 --write-index -o GCA_922984935.2.subset.pacbio.SAMEA7524440.merged_1.minimap2.cram GCA_922984935.2.subset.pacbio.SAMEA7524440.merged_1.minimap2.bam",
+                    "@PG\tID:samtools.4\tPN:samtools\tPP:samtools.3\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.merged_1.minimap2.cram"
+                ]
+            },
             [
                 "pacbio.SAMEA7524440.ERR6939248.hifitrimmer.summary.json:md5,d2d4198c3f7086437249909d94173359",
                 "pacbio.SAMEA7524440.ERR6939249.hifitrimmer.summary.json:md5,83d9985a6d7a4477df704d8f4a23852c"
@@ -386,6 +558,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.4"
         },
-        "timestamp": "2026-05-15T12:13:39.841579495"
+        "timestamp": "2026-05-29T01:57:02.637423352"
     }
 }
\ No newline at end of file
diff --git a/tests/short_aligner_minimap2.nf.test b/tests/short_aligner_minimap2.nf.test
index 964a1537..e129528c 100644
--- a/tests/short_aligner_minimap2.nf.test
+++ b/tests/short_aligner_minimap2.nf.test
@@ -29,6 +29,17 @@ nextflow_pipeline {
             def bam_path = getAllFilesFromDir(params.outdir, include: ['**/*.bam'], relative: true, includeDir: false)
             def fasta = 'https://tolit.cog.sanger.ac.uk/test-data/Meles_meles/assembly/release/mMelMel3.1_paternal_haplotype/GCA_922984935.2.subset.fasta'
 
+            def strip_absolute_path_lines = { text ->
+                def lines = text?.getClass()?.isArray()
+                    ? text.toList()
+                    : (text instanceof Collection ? text : (text?.toString()?.readLines() ?: []))
+                lines
+                    .collect { line ->
+                            line.toString()
+                                .replaceAll(/\bUR:\/((?:[^\/\s]+\/){2})\S+/, 'UR:/$1<ABS_PATH>')
+                    }
+            }
+
             assertAll(
                 { assert workflow.success },
                 { assert snapshot(
@@ -42,6 +53,8 @@ nextflow_pipeline {
                     // Stable mapping files
                     bam_path.collect{ f -> [(new File(f).getName()): bam("${params.outdir}/${f}").getStatistics()] }.collectEntries{ it }.sort(),
                     cram_path.collect{ f -> [(new File(f).getName()): cram("${params.outdir}/${f}", fasta).getStatistics()] }.collectEntries{ it }.sort(),
+                    bam_path.collect{ f -> [(new File(f).getName()): strip_absolute_path_lines(bam("${params.outdir}/${f}").getHeader())] }.collectEntries{ it }.sort(),
+                    cram_path.collect{ f -> [(new File(f).getName()): strip_absolute_path_lines(cram("${params.outdir}/${f}", fasta).getHeader())] }.collectEntries{ it }.sort(),
 
                      // Stable trimming json
                     hifitrimmer_json.collect{ f ->
diff --git a/tests/short_aligner_minimap2.nf.test.snap b/tests/short_aligner_minimap2.nf.test.snap
index f8e9d8b7..c48be2e6 100644
--- a/tests/short_aligner_minimap2.nf.test.snap
+++ b/tests/short_aligner_minimap2.nf.test.snap
@@ -1,7 +1,7 @@
 {
     "-profile test --short_aligner minimap2 --outfmt 'bam,cram'": {
         "content": [
-            77,
+            79,
             {
                 "BGZIP_BEDGRAPH": {
                     "samtools": "1.23.1"
@@ -83,7 +83,7 @@
                     "samtools": "1.23.1"
                 },
                 "Workflow": {
-                    "sanger-tol/readmapping": "v2.0.3"
+                    "sanger-tol/readmapping": "v2.1.0-dev"
                 }
             },
             [
@@ -220,14 +220,99 @@
                     "sorted": false
                 }
             },
+            {
+                "GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.minimap2.bam": [
+                    "@HD\tVN:1.6\tSO:coordinate",
+                    "@SQ\tSN:OV277441.1\tLN:7999920\tM5:0457acf8690429f1c98ee545cb8573b8\tUR:/nfs/treeoflife-01/<ABS_PATH>\tAS:GCA_922984935.2\tAN:SUPER_1\tSP:Meles meles",
+                    "@RG\tID:35528_2#1\tDT:2020-11-17T00:00:00+0000\tPU:201117_A00948_0206_AHGML2DSXY_2#1\tLB:33637906\tPG:SCS\tSM:SAMEA5962964\tCN:SC\tPL:ILLUMINA\tDS:ERP116890: Sequencing and assembly of genomes from British species for the Darwin Tree of Life Project. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ ",
+                    "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t4 -ax sr --cs=short -I1.0G -y -R @RG\\tID:35528_2#1\\tDT:2020-11-17T00:00:00+0000\\tPU:201117_A00948_0206_AHGML2DSXY_2#1\\tLB:33637906\\tPG:SCS\\tSM:SAMEA5962964\\tCN:SC\\tPL:ILLUMINA\\tDS:ERP116890: Sequencing and assembly of genomes from British species for the Darwin Tree of Life Project. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/  GCA_922984935.2.subset.unmasked.mmi -",
+                    "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.22.1\tCL:samtools fixmate -mpu - -",
+                    "@PG\tID:samtools.1\tPN:samtools\tPP:samtools\tVN:1.22.1\tCL:samtools view -h",
+                    "@PG\tID:samtools.2\tPN:samtools\tPP:samtools.1\tVN:1.22.1\tCL:samtools sort --write-index -l1 -@4 -T 35528_2_1.subset.cram.0.SAMEA7524440.ERR6688402_tmp -o 35528_2_1.subset.cram.0.SAMEA7524440.ERR6688402.bam -",
+                    "@PG\tID:samtools.3\tPN:samtools\tPP:samtools.2\tVN:1.23.1\tCL:samtools merge --threads 3 -c -p --reference GCA_922984935.2.subset.unmasked.fa - 1/35528_2_1.subset.cram.0.SAMEA7524440.ERR6688402.bam 2/35528_2_1.subset.cram.1.SAMEA7524440.ERR6688402.bam",
+                    "@PG\tID:samtools.4\tPN:samtools\tPP:samtools.3\tVN:1.23.1\tCL:samtools markdup -T SAMEA7524440.ERR6688402 -f SAMEA7524440.ERR6688402.metrics --threads 4 --reference GCA_922984935.2.subset.unmasked.fa - SAMEA7524440.ERR6688402.bam",
+                    "@PG\tID:crumble\tPN:crumble\tPP:samtools.4\tVN:0.9.1\tCL:crumble -O bam SAMEA7524440.ERR6688402.bam SAMEA7524440.ERR6688402.crumble.bam",
+                    "@PG\tID:samtools.5\tPN:samtools\tPP:crumble\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.minimap2.bam"
+                ],
+                "GCA_922984935.2.subset.illumina.SAMEA7524438.ERR6688599.minimap2.bam": [
+                    "@HD\tVN:1.6\tSO:coordinate",
+                    "@SQ\tSN:OV277441.1\tLN:7999920\tM5:0457acf8690429f1c98ee545cb8573b8\tUR:/nfs/treeoflife-01/<ABS_PATH>\tAS:GCA_922984935.2\tAN:SUPER_1\tSP:Meles meles",
+                    "@RG\tID:31231_3#1\tDT:2019-10-03T01:00:00+0100\tPU:191003_HX4_31231_A_H3353CCX2_3#1\tLB:23687379\tPG:SCS\tSM:SAMEA5962962\tCN:SC\tPL:ILLUMINA\tDS:ERP114452: Sequencing and assembly of vertebrate genomes from British species for the Darwin Tree of Life Project in collaboration with the Vertebrate Genomes Project. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",
+                    "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t4 -ax sr --cs=short -I1.0G -y -R @RG\\tID:31231_3#1\\tDT:2019-10-03T00:00:00+0000\\tPU:191003_HX4_31231_A_H3353CCX2_3#1\\tLB:23687379\\tPG:SCS\\tSM:SAMEA5962962\\tCN:SC\\tPL:ILLUMINA\\tDS:ERP114452: Sequencing and assembly of vertebrate genomes from British species for the Darwin Tree of Life Project in collaboration with the Vertebrate Genomes Project. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ GCA_922984935.2.subset.unmasked.mmi -",
+                    "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.22.1\tCL:samtools fixmate -mpu - -",
+                    "@PG\tID:samtools.1\tPN:samtools\tPP:samtools\tVN:1.22.1\tCL:samtools view -h",
+                    "@PG\tID:samtools.2\tPN:samtools\tPP:samtools.1\tVN:1.22.1\tCL:samtools sort --write-index -l1 -@4 -T SAMEA7524438.ERR6688599.cram.0.SAMEA7524438.ERR6688599_tmp -o SAMEA7524438.ERR6688599.cram.0.SAMEA7524438.ERR6688599.bam -",
+                    "@PG\tID:samtools.3\tPN:samtools\tPP:samtools.2\tVN:1.23.1\tCL:samtools merge --threads 3 -c -p --reference GCA_922984935.2.subset.unmasked.fa - 1/SAMEA7524438.ERR6688599.cram.0.SAMEA7524438.ERR6688599.bam 2/SAMEA7524438.ERR6688599.cram.1.SAMEA7524438.ERR6688599.bam",
+                    "@PG\tID:samtools.4\tPN:samtools\tPP:samtools.3\tVN:1.23.1\tCL:samtools markdup -T SAMEA7524438.ERR6688599 -f SAMEA7524438.ERR6688599.metrics --threads 4 --reference GCA_922984935.2.subset.unmasked.fa - SAMEA7524438.ERR6688599.bam",
+                    "@PG\tID:crumble\tPN:crumble\tPP:samtools.4\tVN:0.9.1\tCL:crumble -O bam SAMEA7524438.ERR6688599.bam SAMEA7524438.ERR6688599.crumble.bam",
+                    "@PG\tID:samtools.5\tPN:samtools\tPP:crumble\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.illumina.SAMEA7524438.ERR6688599.minimap2.bam"
+                ],
+                "GCA_922984935.2.subset.illumina.SAMEA7524439.ERR6688600.minimap2.bam": [
+                    "@HD\tVN:1.6\tSO:coordinate",
+                    "@SQ\tSN:OV277441.1\tLN:7999920\tM5:0457acf8690429f1c98ee545cb8573b8\tUR:/nfs/treeoflife-01/<ABS_PATH>\tAS:GCA_922984935.2\tAN:SUPER_1\tSP:Meles meles",
+                    "@RG\tID:31231_4_1\tPL:ILLUMINA\tSM:SAMEA7524439",
+                    "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t4 -ax sr --cs=short -I1.0G -y -R @RG\\tID:31231_4_1\\tPL:ILLUMINA\\tSM:SAMEA7524439 GCA_922984935.2.subset.unmasked.mmi -",
+                    "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.22.1\tCL:samtools fixmate -mpu - -",
+                    "@PG\tID:samtools.1\tPN:samtools\tPP:samtools\tVN:1.22.1\tCL:samtools view -h",
+                    "@PG\tID:samtools.2\tPN:samtools\tPP:samtools.1\tVN:1.22.1\tCL:samtools sort --write-index -l1 -@4 -T SAMEA7524439.ERR6688600_addRG.cram.0.SAMEA7524439.ERR6688600_tmp -o SAMEA7524439.ERR6688600_addRG.cram.0.SAMEA7524439.ERR6688600.bam -",
+                    "@PG\tID:samtools.3\tPN:samtools\tPP:samtools.2\tVN:1.23.1\tCL:samtools merge --threads 3 -c -p --reference GCA_922984935.2.subset.unmasked.fa - 1/SAMEA7524439.ERR6688600_addRG.cram.0.SAMEA7524439.ERR6688600.bam 2/SAMEA7524439.ERR6688600_addRG.cram.1.SAMEA7524439.ERR6688600.bam",
+                    "@PG\tID:samtools.4\tPN:samtools\tPP:samtools.3\tVN:1.23.1\tCL:samtools markdup -T SAMEA7524439.ERR6688600 -f SAMEA7524439.ERR6688600.metrics --threads 4 --reference GCA_922984935.2.subset.unmasked.fa - SAMEA7524439.ERR6688600.bam",
+                    "@PG\tID:crumble\tPN:crumble\tPP:samtools.4\tVN:0.9.1\tCL:crumble -O bam SAMEA7524439.ERR6688600.bam SAMEA7524439.ERR6688600.crumble.bam",
+                    "@PG\tID:samtools.5\tPN:samtools\tPP:crumble\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.illumina.SAMEA7524439.ERR6688600.minimap2.bam"
+                ]
+            },
+            {
+                "GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.minimap2.cram": [
+                    "@HD\tVN:1.6\tSO:coordinate",
+                    "@SQ\tSN:OV277441.1\tLN:7999920\tM5:0457acf8690429f1c98ee545cb8573b8\tUR:/nfs/treeoflife-01/<ABS_PATH>\tAS:GCA_922984935.2\tAN:SUPER_1\tSP:Meles meles",
+                    "@RG\tID:35528_2#1\tDT:2020-11-17T00:00:00+0000\tPU:201117_A00948_0206_AHGML2DSXY_2#1\tLB:33637906\tPG:SCS\tSM:SAMEA5962964\tCN:SC\tPL:ILLUMINA\tDS:ERP116890: Sequencing and assembly of genomes from British species for the Darwin Tree of Life Project. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ ",
+                    "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t4 -ax sr --cs=short -I1.0G -y -R @RG\\tID:35528_2#1\\tDT:2020-11-17T00:00:00+0000\\tPU:201117_A00948_0206_AHGML2DSXY_2#1\\tLB:33637906\\tPG:SCS\\tSM:SAMEA5962964\\tCN:SC\\tPL:ILLUMINA\\tDS:ERP116890: Sequencing and assembly of genomes from British species for the Darwin Tree of Life Project. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/  GCA_922984935.2.subset.unmasked.mmi -",
+                    "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.22.1\tCL:samtools fixmate -mpu - -",
+                    "@PG\tID:samtools.1\tPN:samtools\tPP:samtools\tVN:1.22.1\tCL:samtools view -h",
+                    "@PG\tID:samtools.2\tPN:samtools\tPP:samtools.1\tVN:1.22.1\tCL:samtools sort --write-index -l1 -@4 -T 35528_2_1.subset.cram.0.SAMEA7524440.ERR6688402_tmp -o 35528_2_1.subset.cram.0.SAMEA7524440.ERR6688402.bam -",
+                    "@PG\tID:samtools.3\tPN:samtools\tPP:samtools.2\tVN:1.23.1\tCL:samtools merge --threads 3 -c -p --reference GCA_922984935.2.subset.unmasked.fa - 1/35528_2_1.subset.cram.0.SAMEA7524440.ERR6688402.bam 2/35528_2_1.subset.cram.1.SAMEA7524440.ERR6688402.bam",
+                    "@PG\tID:samtools.4\tPN:samtools\tPP:samtools.3\tVN:1.23.1\tCL:samtools markdup -T SAMEA7524440.ERR6688402 -f SAMEA7524440.ERR6688402.metrics --threads 4 --reference GCA_922984935.2.subset.unmasked.fa - SAMEA7524440.ERR6688402.bam",
+                    "@PG\tID:crumble\tPN:crumble\tPP:samtools.4\tVN:0.9.1\tCL:crumble -O bam SAMEA7524440.ERR6688402.bam SAMEA7524440.ERR6688402.crumble.bam",
+                    "@PG\tID:samtools.5\tPN:samtools\tPP:crumble\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1,lossy_names=1 --write-index -o GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.minimap2.cram GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.minimap2.bam",
+                    "@PG\tID:samtools.6\tPN:samtools\tPP:samtools.5\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.minimap2.cram"
+                ],
+                "GCA_922984935.2.subset.illumina.SAMEA7524438.ERR6688599.minimap2.cram": [
+                    "@HD\tVN:1.6\tSO:coordinate",
+                    "@SQ\tSN:OV277441.1\tLN:7999920\tM5:0457acf8690429f1c98ee545cb8573b8\tUR:/nfs/treeoflife-01/<ABS_PATH>\tAS:GCA_922984935.2\tAN:SUPER_1\tSP:Meles meles",
+                    "@RG\tID:31231_3#1\tDT:2019-10-03T01:00:00+0100\tPU:191003_HX4_31231_A_H3353CCX2_3#1\tLB:23687379\tPG:SCS\tSM:SAMEA5962962\tCN:SC\tPL:ILLUMINA\tDS:ERP114452: Sequencing and assembly of vertebrate genomes from British species for the Darwin Tree of Life Project in collaboration with the Vertebrate Genomes Project. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",
+                    "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t4 -ax sr --cs=short -I1.0G -y -R @RG\\tID:31231_3#1\\tDT:2019-10-03T00:00:00+0000\\tPU:191003_HX4_31231_A_H3353CCX2_3#1\\tLB:23687379\\tPG:SCS\\tSM:SAMEA5962962\\tCN:SC\\tPL:ILLUMINA\\tDS:ERP114452: Sequencing and assembly of vertebrate genomes from British species for the Darwin Tree of Life Project in collaboration with the Vertebrate Genomes Project. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ GCA_922984935.2.subset.unmasked.mmi -",
+                    "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.22.1\tCL:samtools fixmate -mpu - -",
+                    "@PG\tID:samtools.1\tPN:samtools\tPP:samtools\tVN:1.22.1\tCL:samtools view -h",
+                    "@PG\tID:samtools.2\tPN:samtools\tPP:samtools.1\tVN:1.22.1\tCL:samtools sort --write-index -l1 -@4 -T SAMEA7524438.ERR6688599.cram.0.SAMEA7524438.ERR6688599_tmp -o SAMEA7524438.ERR6688599.cram.0.SAMEA7524438.ERR6688599.bam -",
+                    "@PG\tID:samtools.3\tPN:samtools\tPP:samtools.2\tVN:1.23.1\tCL:samtools merge --threads 3 -c -p --reference GCA_922984935.2.subset.unmasked.fa - 1/SAMEA7524438.ERR6688599.cram.0.SAMEA7524438.ERR6688599.bam 2/SAMEA7524438.ERR6688599.cram.1.SAMEA7524438.ERR6688599.bam",
+                    "@PG\tID:samtools.4\tPN:samtools\tPP:samtools.3\tVN:1.23.1\tCL:samtools markdup -T SAMEA7524438.ERR6688599 -f SAMEA7524438.ERR6688599.metrics --threads 4 --reference GCA_922984935.2.subset.unmasked.fa - SAMEA7524438.ERR6688599.bam",
+                    "@PG\tID:crumble\tPN:crumble\tPP:samtools.4\tVN:0.9.1\tCL:crumble -O bam SAMEA7524438.ERR6688599.bam SAMEA7524438.ERR6688599.crumble.bam",
+                    "@PG\tID:samtools.5\tPN:samtools\tPP:crumble\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1,lossy_names=1 --write-index -o GCA_922984935.2.subset.illumina.SAMEA7524438.ERR6688599.minimap2.cram GCA_922984935.2.subset.illumina.SAMEA7524438.ERR6688599.minimap2.bam",
+                    "@PG\tID:samtools.6\tPN:samtools\tPP:samtools.5\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.illumina.SAMEA7524438.ERR6688599.minimap2.cram"
+                ],
+                "GCA_922984935.2.subset.illumina.SAMEA7524439.ERR6688600.minimap2.cram": [
+                    "@HD\tVN:1.6\tSO:coordinate",
+                    "@SQ\tSN:OV277441.1\tLN:7999920\tM5:0457acf8690429f1c98ee545cb8573b8\tUR:/nfs/treeoflife-01/<ABS_PATH>\tAS:GCA_922984935.2\tAN:SUPER_1\tSP:Meles meles",
+                    "@RG\tID:31231_4_1\tPL:ILLUMINA\tSM:SAMEA7524439",
+                    "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t4 -ax sr --cs=short -I1.0G -y -R @RG\\tID:31231_4_1\\tPL:ILLUMINA\\tSM:SAMEA7524439 GCA_922984935.2.subset.unmasked.mmi -",
+                    "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.22.1\tCL:samtools fixmate -mpu - -",
+                    "@PG\tID:samtools.1\tPN:samtools\tPP:samtools\tVN:1.22.1\tCL:samtools view -h",
+                    "@PG\tID:samtools.2\tPN:samtools\tPP:samtools.1\tVN:1.22.1\tCL:samtools sort --write-index -l1 -@4 -T SAMEA7524439.ERR6688600_addRG.cram.0.SAMEA7524439.ERR6688600_tmp -o SAMEA7524439.ERR6688600_addRG.cram.0.SAMEA7524439.ERR6688600.bam -",
+                    "@PG\tID:samtools.3\tPN:samtools\tPP:samtools.2\tVN:1.23.1\tCL:samtools merge --threads 3 -c -p --reference GCA_922984935.2.subset.unmasked.fa - 1/SAMEA7524439.ERR6688600_addRG.cram.0.SAMEA7524439.ERR6688600.bam 2/SAMEA7524439.ERR6688600_addRG.cram.1.SAMEA7524439.ERR6688600.bam",
+                    "@PG\tID:samtools.4\tPN:samtools\tPP:samtools.3\tVN:1.23.1\tCL:samtools markdup -T SAMEA7524439.ERR6688600 -f SAMEA7524439.ERR6688600.metrics --threads 4 --reference GCA_922984935.2.subset.unmasked.fa - SAMEA7524439.ERR6688600.bam",
+                    "@PG\tID:crumble\tPN:crumble\tPP:samtools.4\tVN:0.9.1\tCL:crumble -O bam SAMEA7524439.ERR6688600.bam SAMEA7524439.ERR6688600.crumble.bam",
+                    "@PG\tID:samtools.5\tPN:samtools\tPP:crumble\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1,lossy_names=1 --write-index -o GCA_922984935.2.subset.illumina.SAMEA7524439.ERR6688600.minimap2.cram GCA_922984935.2.subset.illumina.SAMEA7524439.ERR6688600.minimap2.bam",
+                    "@PG\tID:samtools.6\tPN:samtools\tPP:samtools.5\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.illumina.SAMEA7524439.ERR6688600.minimap2.cram"
+                ]
+            },
             [
-
+                
             ]
         ],
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.10.4"
         },
-        "timestamp": "2026-04-29T19:13:10.330631613"
+        "timestamp": "2026-05-29T01:22:33.94399251"
     }
-}
+}
\ No newline at end of file
diff --git a/tests/uli.nf.test b/tests/uli.nf.test
index 1438f913..befcb382 100644
--- a/tests/uli.nf.test
+++ b/tests/uli.nf.test
@@ -27,6 +27,18 @@ nextflow_pipeline {
             def bam_path = getAllFilesFromDir(params.outdir, include: ['**/*.bam'], relative: true, includeDir: false)
             def fasta = 'https://tolit.cog.sanger.ac.uk/test-data/Meles_meles/assembly/release/mMelMel3.1_paternal_haplotype/GCA_922984935.2.subset.fasta'
 
+            def strip_absolute_path_lines = { text ->
+                def lines = text?.getClass()?.isArray()
+                    ? text.toList()
+                    : (text instanceof Collection ? text : (text?.toString()?.readLines() ?: []))
+                lines
+                    .collect { line ->
+                        line.toString()
+                            .replaceAll(/\bUR:\/(?:([^\/\s]+)\/([^\/\s]+)\/([^\/\s]+))\/\S+/, 'UR:/$1/$2/$3/<ABS_PATH>')
+                            .replaceAll(/(^|\s)\/(?:[^\s\/]+\/)+[^\s\/]+/, '$1<ABS_PATH>')
+                    }
+            }
+
             assertAll(
                 { assert workflow.success},
                 { assert snapshot(
@@ -40,6 +52,8 @@ nextflow_pipeline {
                     // Stable mapping files
                     bam_path.collect{ f -> [(new File(f).getName()): bam("${params.outdir}/${f}").getStatistics()] }.collectEntries{ it }.sort(),
                     cram_path.collect{ f -> [(new File(f).getName()): cram("${params.outdir}/${f}", fasta).getStatistics()] }.collectEntries{ it }.sort(),
+                    bam_path.collect{ f -> [(new File(f).getName()): strip_absolute_path_lines(bam("${params.outdir}/${f}").getHeader())] }.collectEntries{ it }.sort(),
+                    cram_path.collect{ f -> [(new File(f).getName()): strip_absolute_path_lines(cram("${params.outdir}/${f}", fasta).getHeader())] }.collectEntries{ it }.sort(),
 
                      // Stable trimming json
                     hifitrimmer_json.collect{ f ->
diff --git a/tests/uli.nf.test.snap b/tests/uli.nf.test.snap
index 7b8bbf66..cbc2ae1b 100644
--- a/tests/uli.nf.test.snap
+++ b/tests/uli.nf.test.snap
@@ -85,7 +85,7 @@
                     "samtools": "1.23.1"
                 },
                 "Workflow": {
-                    "sanger-tol/readmapping": "v2.0.3"
+                    "sanger-tol/readmapping": "v2.1.0-dev"
                 }
             },
             [
@@ -143,7 +143,7 @@
                 "GCA_964034985.1.subset.pacbio.SAMEA114784749.ERR14209104_test.minimap2.stats.gz:md5,4f5930c586e221b776fdd20394b18700"
             ],
             {
-
+                
             },
             {
                 "GCA_964034985.1.subset.pacbio.SAMEA114784749.ERR14209104.minimap2.cram": {
@@ -169,6 +169,37 @@
                     "sorted": false
                 }
             },
+            {
+                
+            },
+            {
+                "GCA_964034985.1.subset.pacbio.SAMEA114784749.ERR14209104.minimap2.cram": [
+                    "@HD\tVN:1.6\tSO:coordinate",
+                    "@SQ\tSN:CAXIUN010000020.1\tLN:15094\tM5:eb4b4e09fa2962e012fc983eeb6b65dc\tUR:/lustre/scratch124/tol/<ABS_PATH>",
+                    "@SQ\tSN:CAXIUN010000038.1\tLN:1000\tM5:3fe8a9b5a85c60b19e74e88ca5ca434e\tUR:/lustre/scratch124/tol/<ABS_PATH>",
+                    "@SQ\tSN:CAXIUN010000104.1\tLN:10110\tM5:10013ae295fb0e1a002ab812d6c2e77e\tUR:/lustre/scratch124/tol/<ABS_PATH>",
+                    "@SQ\tSN:CAXIUN010000129.1\tLN:29940\tM5:9579779c87681c88e68a924f572f5599\tUR:/lustre/scratch124/tol/<ABS_PATH>",
+                    "@RG\tID:0de7f0a4/27--27\tPL:PACBIO\tDS:READTYPE=CCS;Ipd:CodecV1=ip;PulseWidth:CodecV1=pw;BINDINGKIT=102-739-100;SEQUENCINGKIT=102-118-800;BASECALLERVERSION=5.0;SMRTCELLKIT=102-202-200;SMRTCELLID=EA138735;RUNID=r84093_20241115_102726;ICSVERSION=13.0.0.212033;MOVIELENGTH=1440.0;FRAMERATEHZ=100.000000;BarcodeFile=metadata/m84093_241116_151316_s2.barcodes.fasta;BarcodeHash=86d73e586a6d3ede0295785b51105eea;BarcodeCount=96;BarcodeMode=Symmetric;BarcodeQuality=Score\tLB:TRAC-2-8053\tPU:m84093_241116_151316_s2\tSM:TOL_ASG14652249\tPM:REVIO\tBC:ACTGCAGCACGAGTAT\tCM:R/P1-C1/5.0-25M",
+                    "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t4 -ax map-hifi --cs=short -y -R @RG\\tID:0de7f0a4/27--27\\tPL:PACBIO\\tDS:READTYPE=CCS;Ipd:CodecV1=ip;PulseWidth:CodecV1=pw;BINDINGKIT=102-739-100;SEQUENCINGKIT=102-118-800;BASECALLERVERSION=5.0;SMRTCELLKIT=102-202-200;SMRTCELLID=EA138735;RUNID=r84093_20241115_102726;ICSVERSION=13.0.0.212033;MOVIELENGTH=1440.0;FRAMERATEHZ=100.000000;BarcodeFile=metadata/m84093_241116_151316_s2.barcodes.fasta;BarcodeHash=86d73e586a6d3ede0295785b51105eea;BarcodeCount=96;BarcodeMode=Symmetric;BarcodeQuality=Score\\tLB:TRAC-2-8053\\tPU:m84093_241116_151316_s2\\tSM:TOL_ASG14652249\\tPM:REVIO\\tBC:ACTGCAGCACGAGTAT\\tCM:R/P1-C1/5.0-25M -I1G -a GCA_964034985.1.subset.unmasked.mmi -",
+                    "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.23.1\tCL:samtools sort -@ 3 -o pacbio.SAMEA114784749.ERR14209104.hifitrimmer.fastq.gz.0.SAMEA114784749.ERR14209104.bam -T pacbio.SAMEA114784749.ERR14209104.hifitrimmer.fastq.gz.0.SAMEA114784749.ERR14209104_sort_tmp --write-index -l1 -",
+                    "@PG\tID:samtools.1\tPN:samtools\tPP:samtools\tVN:1.23.1\tCL:samtools merge --threads 3 -c -p --reference GCA_964034985.1.subset.unmasked.fa SAMEA114784749.ERR14209104.merge.bam 1/pacbio.SAMEA114784749.ERR14209104.hifitrimmer.fastq.gz.0.SAMEA114784749.ERR14209104.bam 2/pacbio.SAMEA114784749.ERR14209104.hifitrimmer.fastq.gz.1.SAMEA114784749.ERR14209104.bam 3/pacbio.SAMEA114784749.ERR14209104.hifitrimmer.fastq.gz.2.SAMEA114784749.ERR14209104.bam 4/pacbio.SAMEA114784749.ERR14209104.hifitrimmer.fastq.gz.3.SAMEA114784749.ERR14209104.bam 5/pacbio.SAMEA114784749.ERR14209104.hifitrimmer.fastq.gz.4.SAMEA114784749.ERR14209104.bam",
+                    "@PG\tID:crumble\tPN:crumble\tPP:samtools.1\tVN:0.9.1\tCL:crumble -y pbccs -O bam SAMEA114784749.ERR14209104.merge.bam SAMEA114784749.ERR14209104.merge.crumble.bam",
+                    "@PG\tID:samtools.2\tPN:samtools\tPP:crumble\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_964034985.1.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1 --write-index -o GCA_964034985.1.subset.pacbio.SAMEA114784749.ERR14209104.minimap2.cram GCA_964034985.1.subset.pacbio.SAMEA114784749.ERR14209104.minimap2.bam"
+                ],
+                "GCA_964034985.1.subset.pacbio.SAMEA114784749.ERR14209104_test.minimap2.cram": [
+                    "@HD\tVN:1.6\tSO:coordinate",
+                    "@SQ\tSN:CAXIUN010000020.1\tLN:15094\tM5:eb4b4e09fa2962e012fc983eeb6b65dc\tUR:/lustre/scratch124/tol/<ABS_PATH>",
+                    "@SQ\tSN:CAXIUN010000038.1\tLN:1000\tM5:3fe8a9b5a85c60b19e74e88ca5ca434e\tUR:/lustre/scratch124/tol/<ABS_PATH>",
+                    "@SQ\tSN:CAXIUN010000104.1\tLN:10110\tM5:10013ae295fb0e1a002ab812d6c2e77e\tUR:/lustre/scratch124/tol/<ABS_PATH>",
+                    "@SQ\tSN:CAXIUN010000129.1\tLN:29940\tM5:9579779c87681c88e68a924f572f5599\tUR:/lustre/scratch124/tol/<ABS_PATH>",
+                    "@RG\tID:0de7f0a4/27--27\tPL:PACBIO\tDS:READTYPE=CCS;Ipd:CodecV1=ip;PulseWidth:CodecV1=pw;BINDINGKIT=102-739-100;SEQUENCINGKIT=102-118-800;BASECALLERVERSION=5.0;SMRTCELLKIT=102-202-200;SMRTCELLID=EA138735;RUNID=r84093_20241115_102726;ICSVERSION=13.0.0.212033;MOVIELENGTH=1440.0;FRAMERATEHZ=100.000000;BarcodeFile=metadata/m84093_241116_151316_s2.barcodes.fasta;BarcodeHash=86d73e586a6d3ede0295785b51105eea;BarcodeCount=96;BarcodeMode=Symmetric;BarcodeQuality=Score\tLB:TRAC-2-8053\tPU:m84093_241116_151316_s2\tSM:TOL_ASG14652249\tPM:REVIO\tBC:ACTGCAGCACGAGTAT\tCM:R/P1-C1/5.0-25M",
+                    "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t4 -ax map-hifi --cs=short -y -R @RG\\tID:0de7f0a4/27--27\\tPL:PACBIO\\tDS:READTYPE=CCS;Ipd:CodecV1=ip;PulseWidth:CodecV1=pw;BINDINGKIT=102-739-100;SEQUENCINGKIT=102-118-800;BASECALLERVERSION=5.0;SMRTCELLKIT=102-202-200;SMRTCELLID=EA138735;RUNID=r84093_20241115_102726;ICSVERSION=13.0.0.212033;MOVIELENGTH=1440.0;FRAMERATEHZ=100.000000;BarcodeFile=metadata/m84093_241116_151316_s2.barcodes.fasta;BarcodeHash=86d73e586a6d3ede0295785b51105eea;BarcodeCount=96;BarcodeMode=Symmetric;BarcodeQuality=Score\\tLB:TRAC-2-8053\\tPU:m84093_241116_151316_s2\\tSM:TOL_ASG14652249\\tPM:REVIO\\tBC:ACTGCAGCACGAGTAT\\tCM:R/P1-C1/5.0-25M -I1G -a GCA_964034985.1.subset.unmasked.mmi -",
+                    "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.23.1\tCL:samtools sort -@ 3 -o pacbio.SAMEA114784749.ERR14209104_test.hifitrimmer.fastq.gz.0.SAMEA114784749.ERR14209104_test.bam -T pacbio.SAMEA114784749.ERR14209104_test.hifitrimmer.fastq.gz.0.SAMEA114784749.ERR14209104_test_sort_tmp --write-index -l1 -",
+                    "@PG\tID:samtools.1\tPN:samtools\tPP:samtools\tVN:1.23.1\tCL:samtools merge --threads 3 -c -p --reference GCA_964034985.1.subset.unmasked.fa SAMEA114784749.ERR14209104_test.merge.bam 1/pacbio.SAMEA114784749.ERR14209104_test.hifitrimmer.fastq.gz.0.SAMEA114784749.ERR14209104_test.bam",
+                    "@PG\tID:crumble\tPN:crumble\tPP:samtools.1\tVN:0.9.1\tCL:crumble -y pbccs -O bam SAMEA114784749.ERR14209104_test.merge.bam SAMEA114784749.ERR14209104_test.merge.crumble.bam",
+                    "@PG\tID:samtools.2\tPN:samtools\tPP:crumble\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_964034985.1.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1 --write-index -o GCA_964034985.1.subset.pacbio.SAMEA114784749.ERR14209104_test.minimap2.cram GCA_964034985.1.subset.pacbio.SAMEA114784749.ERR14209104_test.minimap2.bam"
+                ]
+            },
             [
                 "pacbio.SAMEA114784749.ERR14209104.hifitrimmer.summary.json:md5,238e515a0593f4c66e74bff41a33b63c",
                 "pacbio.SAMEA114784749.ERR14209104_test.hifitrimmer.summary.json:md5,4ab835890a22ca1dd2206300f30fbc27"
@@ -178,6 +209,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.4"
         },
-        "timestamp": "2026-04-29T19:20:07.06121781"
+        "timestamp": "2026-05-29T00:46:30.255398793"
     }
-}
+}
\ No newline at end of file
diff --git a/tests/uli_no_lima.nf.test b/tests/uli_no_lima.nf.test
index 0efc9e1f..7db645a8 100644
--- a/tests/uli_no_lima.nf.test
+++ b/tests/uli_no_lima.nf.test
@@ -29,6 +29,18 @@ nextflow_pipeline {
             def bam_path = getAllFilesFromDir(params.outdir, include: ['**/*.bam'], relative: true, includeDir: false)
             def fasta = 'https://tolit.cog.sanger.ac.uk/test-data/Meles_meles/assembly/release/mMelMel3.1_paternal_haplotype/GCA_922984935.2.subset.fasta'
 
+            def strip_absolute_path_lines = { text ->
+                def lines = text?.getClass()?.isArray()
+                    ? text.toList()
+                    : (text instanceof Collection ? text : (text?.toString()?.readLines() ?: []))
+                lines
+                    .collect { line ->
+                        line.toString()
+                            .replaceAll(/\bUR:\/(?:([^\/\s]+)\/([^\/\s]+)\/([^\/\s]+))\/\S+/, 'UR:/$1/$2/$3/<ABS_PATH>')
+                            .replaceAll(/(^|\s)\/(?:[^\s\/]+\/)+[^\s\/]+/, '$1<ABS_PATH>')
+                    }
+            }
+
             assertAll(
                 { assert workflow.success},
                 { assert snapshot(
@@ -42,6 +54,8 @@ nextflow_pipeline {
                     // Stable mapping files
                     bam_path.collect{ f -> [(new File(f).getName()): bam("${params.outdir}/${f}").getStatistics()] }.collectEntries{ it }.sort(),
                     cram_path.collect{ f -> [(new File(f).getName()): cram("${params.outdir}/${f}", fasta).getStatistics()] }.collectEntries{ it }.sort(),
+                    bam_path.collect{ f -> [(new File(f).getName()): strip_absolute_path_lines(bam("${params.outdir}/${f}").getHeader())] }.collectEntries{ it }.sort(),
+                    cram_path.collect{ f -> [(new File(f).getName()): strip_absolute_path_lines(cram("${params.outdir}/${f}", fasta).getHeader())] }.collectEntries{ it }.sort(),
 
                      // Stable trimming json
                     hifitrimmer_json.collect{ f ->
diff --git a/tests/uli_no_lima.nf.test.snap b/tests/uli_no_lima.nf.test.snap
index 1e08831b..ab978f72 100644
--- a/tests/uli_no_lima.nf.test.snap
+++ b/tests/uli_no_lima.nf.test.snap
@@ -82,7 +82,7 @@
                     "samtools": "1.23.1"
                 },
                 "Workflow": {
-                    "sanger-tol/readmapping": "v2.0.3"
+                    "sanger-tol/readmapping": "v2.1.0-dev"
                 }
             },
             [
@@ -162,7 +162,36 @@
                 }
             },
             {
-
+                
+            },
+            {
+                "GCA_964034985.1.subset.pacbio.SAMEA114784749.ERR14209104.minimap2.bam": [
+                    "@HD\tVN:1.6\tSO:coordinate",
+                    "@SQ\tSN:CAXIUN010000020.1\tLN:15094",
+                    "@SQ\tSN:CAXIUN010000038.1\tLN:1000",
+                    "@SQ\tSN:CAXIUN010000104.1\tLN:10110",
+                    "@SQ\tSN:CAXIUN010000129.1\tLN:29940",
+                    "@RG\tID:0de7f0a4/27--27\tPL:PACBIO\tDS:READTYPE=CCS;Ipd:CodecV1=ip;PulseWidth:CodecV1=pw;BINDINGKIT=102-739-100;SEQUENCINGKIT=102-118-800;BASECALLERVERSION=5.0;SMRTCELLKIT=102-202-200;SMRTCELLID=EA138735;RUNID=r84093_20241115_102726;ICSVERSION=13.0.0.212033;MOVIELENGTH=1440.0;FRAMERATEHZ=100.000000;BarcodeFile=metadata/m84093_241116_151316_s2.barcodes.fasta;BarcodeHash=86d73e586a6d3ede0295785b51105eea;BarcodeCount=96;BarcodeMode=Symmetric;BarcodeQuality=Score\tLB:TRAC-2-8053\tPU:m84093_241116_151316_s2\tSM:TOL_ASG14652249\tPM:REVIO\tBC:ACTGCAGCACGAGTAT\tCM:R/P1-C1/5.0-25M",
+                    "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t4 -ax map-hifi --cs=short -y -R @RG\\tID:0de7f0a4/27--27\\tPL:PACBIO\\tDS:READTYPE=CCS;Ipd:CodecV1=ip;PulseWidth:CodecV1=pw;BINDINGKIT=102-739-100;SEQUENCINGKIT=102-118-800;BASECALLERVERSION=5.0;SMRTCELLKIT=102-202-200;SMRTCELLID=EA138735;RUNID=r84093_20241115_102726;ICSVERSION=13.0.0.212033;MOVIELENGTH=1440.0;FRAMERATEHZ=100.000000;BarcodeFile=metadata/m84093_241116_151316_s2.barcodes.fasta;BarcodeHash=86d73e586a6d3ede0295785b51105eea;BarcodeCount=96;BarcodeMode=Symmetric;BarcodeQuality=Score\\tLB:TRAC-2-8053\\tPU:m84093_241116_151316_s2\\tSM:TOL_ASG14652249\\tPM:REVIO\\tBC:ACTGCAGCACGAGTAT\\tCM:R/P1-C1/5.0-25M -I1G -a GCA_964034985.1.subset.unmasked.mmi -",
+                    "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.23.1\tCL:samtools sort -@ 3 -o pacbio.SAMEA114784749.ERR14209104.hifitrimmer.fastq.gz.0.SAMEA114784749.ERR14209104.bam -T pacbio.SAMEA114784749.ERR14209104.hifitrimmer.fastq.gz.0.SAMEA114784749.ERR14209104_sort_tmp --write-index -l1 -",
+                    "@PG\tID:samtools.1\tPN:samtools\tPP:samtools\tVN:1.23.1\tCL:samtools merge --threads 3 -c -p --reference GCA_964034985.1.subset.unmasked.fa SAMEA114784749.ERR14209104.merge.bam 1/pacbio.SAMEA114784749.ERR14209104.hifitrimmer.fastq.gz.0.SAMEA114784749.ERR14209104.bam",
+                    "@PG\tID:crumble\tPN:crumble\tPP:samtools.1\tVN:0.9.1\tCL:crumble -y pbccs -O bam SAMEA114784749.ERR14209104.merge.bam SAMEA114784749.ERR14209104.merge.crumble.bam"
+                ],
+                "GCA_964034985.1.subset.pacbio.SAMEA114784749.ERR14209104_test.minimap2.bam": [
+                    "@HD\tVN:1.6\tSO:coordinate",
+                    "@SQ\tSN:CAXIUN010000020.1\tLN:15094",
+                    "@SQ\tSN:CAXIUN010000038.1\tLN:1000",
+                    "@SQ\tSN:CAXIUN010000104.1\tLN:10110",
+                    "@SQ\tSN:CAXIUN010000129.1\tLN:29940",
+                    "@RG\tID:0de7f0a4/27--27\tPL:PACBIO\tDS:READTYPE=CCS;Ipd:CodecV1=ip;PulseWidth:CodecV1=pw;BINDINGKIT=102-739-100;SEQUENCINGKIT=102-118-800;BASECALLERVERSION=5.0;SMRTCELLKIT=102-202-200;SMRTCELLID=EA138735;RUNID=r84093_20241115_102726;ICSVERSION=13.0.0.212033;MOVIELENGTH=1440.0;FRAMERATEHZ=100.000000;BarcodeFile=metadata/m84093_241116_151316_s2.barcodes.fasta;BarcodeHash=86d73e586a6d3ede0295785b51105eea;BarcodeCount=96;BarcodeMode=Symmetric;BarcodeQuality=Score\tLB:TRAC-2-8053\tPU:m84093_241116_151316_s2\tSM:TOL_ASG14652249\tPM:REVIO\tBC:ACTGCAGCACGAGTAT\tCM:R/P1-C1/5.0-25M",
+                    "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t4 -ax map-hifi --cs=short -y -R @RG\\tID:0de7f0a4/27--27\\tPL:PACBIO\\tDS:READTYPE=CCS;Ipd:CodecV1=ip;PulseWidth:CodecV1=pw;BINDINGKIT=102-739-100;SEQUENCINGKIT=102-118-800;BASECALLERVERSION=5.0;SMRTCELLKIT=102-202-200;SMRTCELLID=EA138735;RUNID=r84093_20241115_102726;ICSVERSION=13.0.0.212033;MOVIELENGTH=1440.0;FRAMERATEHZ=100.000000;BarcodeFile=metadata/m84093_241116_151316_s2.barcodes.fasta;BarcodeHash=86d73e586a6d3ede0295785b51105eea;BarcodeCount=96;BarcodeMode=Symmetric;BarcodeQuality=Score\\tLB:TRAC-2-8053\\tPU:m84093_241116_151316_s2\\tSM:TOL_ASG14652249\\tPM:REVIO\\tBC:ACTGCAGCACGAGTAT\\tCM:R/P1-C1/5.0-25M -I1G -a GCA_964034985.1.subset.unmasked.mmi -",
+                    "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.23.1\tCL:samtools sort -@ 3 -o pacbio.SAMEA114784749.ERR14209104_test.hifitrimmer.fastq.gz.0.SAMEA114784749.ERR14209104_test.bam -T pacbio.SAMEA114784749.ERR14209104_test.hifitrimmer.fastq.gz.0.SAMEA114784749.ERR14209104_test_sort_tmp --write-index -l1 -",
+                    "@PG\tID:samtools.1\tPN:samtools\tPP:samtools\tVN:1.23.1\tCL:samtools merge --threads 3 -c -p --reference GCA_964034985.1.subset.unmasked.fa SAMEA114784749.ERR14209104_test.merge.bam 1/pacbio.SAMEA114784749.ERR14209104_test.hifitrimmer.fastq.gz.0.SAMEA114784749.ERR14209104_test.bam",
+                    "@PG\tID:crumble\tPN:crumble\tPP:samtools.1\tVN:0.9.1\tCL:crumble -y pbccs -O bam SAMEA114784749.ERR14209104_test.merge.bam SAMEA114784749.ERR14209104_test.merge.crumble.bam"
+                ]
+            },
+            {
+                
             },
             [
                 "pacbio.SAMEA114784749.ERR14209104.hifitrimmer.summary.json:md5,f8d293d48de8a48ba7b1bffa56b5ab89",
@@ -173,6 +202,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.4"
         },
-        "timestamp": "2026-04-29T19:16:58.80829055"
+        "timestamp": "2026-05-28T20:23:05.002283734"
     }
-}
+}
\ No newline at end of file
diff --git a/tests/untrim.nf.test b/tests/untrim.nf.test
index c776ae42..d1736f4a 100644
--- a/tests/untrim.nf.test
+++ b/tests/untrim.nf.test
@@ -31,6 +31,18 @@ nextflow_pipeline {
             def bam_path = getAllFilesFromDir(params.outdir, include: ['**/*.bam'], relative: true, includeDir: false)
             def fasta = 'https://tolit.cog.sanger.ac.uk/test-data/Meles_meles/assembly/release/mMelMel3.1_paternal_haplotype/GCA_922984935.2.subset.fasta'
 
+            def strip_absolute_path_lines = { text ->
+                def lines = text?.getClass()?.isArray()
+                    ? text.toList()
+                    : (text instanceof Collection ? text : (text?.toString()?.readLines() ?: []))
+                lines
+                    .collect { line ->
+                        line.toString()
+                            .replaceAll(/\bUR:\/(?:([^\/\s]+)\/([^\/\s]+)\/([^\/\s]+))\/\S+/, 'UR:/$1/$2/$3/<ABS_PATH>')
+                            .replaceAll(/(^|\s)\/(?:[^\s\/]+\/)+[^\s\/]+/, '$1<ABS_PATH>')
+                    }
+            }
+
             assertAll(
                 { assert workflow.success},
                 { assert snapshot(
@@ -44,6 +56,8 @@ nextflow_pipeline {
                     // Stable mapping files
                     bam_path.collect{ f -> [(new File(f).getName()): bam("${params.outdir}/${f}").getStatistics()] }.collectEntries{ it }.sort(),
                     cram_path.collect{ f -> [(new File(f).getName()): cram("${params.outdir}/${f}", fasta).getStatistics()] }.collectEntries{ it }.sort(),
+                    bam_path.collect{ f -> [(new File(f).getName()): strip_absolute_path_lines(bam("${params.outdir}/${f}").getHeader())] }.collectEntries{ it }.sort(),
+                    cram_path.collect{ f -> [(new File(f).getName()): strip_absolute_path_lines(cram("${params.outdir}/${f}", fasta).getHeader())] }.collectEntries{ it }.sort(),
 
                      // Stable trimming json
                     hifitrimmer_json.collect{ f ->
diff --git a/tests/untrim.nf.test.snap b/tests/untrim.nf.test.snap
index c85069e7..5ebff3c9 100644
--- a/tests/untrim.nf.test.snap
+++ b/tests/untrim.nf.test.snap
@@ -1,7 +1,7 @@
 {
     "-profile test --pacbio_adapter_fasta false --pacbio_adapter_yaml false --outfmt bam": {
         "content": [
-            68,
+            70,
             {
                 "BGZIP_BEDGRAPH": {
                     "samtools": "1.23.1"
@@ -39,6 +39,9 @@
                 "MINIMAP2_INDEX": {
                     "minimap2": "2.30-r1287"
                 },
+                "SAMTOOLS_ADD_PG": {
+                    "samtools": "1.23.1"
+                },
                 "SAMTOOLS_FAIDX": {
                     "samtools": "1.23.1"
                 },
@@ -67,7 +70,7 @@
                     "samtools": "1.23.1"
                 },
                 "Workflow": {
-                    "sanger-tol/readmapping": "v2.0.3"
+                    "sanger-tol/readmapping": "v2.1.0-dev"
                 }
             },
             [
@@ -192,16 +195,72 @@
                 }
             },
             {
-
+                
+            },
+            {
+                "GCA_922984935.2.subset.ont.SAMEA7524440.PAE35587.minimap2.bam": [
+                    "@HD\tVN:1.6\tSO:coordinate",
+                    "@SQ\tSN:OV277441.1\tLN:7999920\tM5:0457acf8690429f1c98ee545cb8573b8\tUR:/nfs/treeoflife-01/resources/<ABS_PATH>\tAS:GCA_922984935.2\tAN:SUPER_1\tSP:Meles meles",
+                    "@RG\tID:PAE35587_pass_1f1f0707_115\tPL:ONT\tSM:SAMEA7524440",
+                    "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t4 -ax map-ont -y -R @RG\\tID:PAE35587_pass_1f1f0707_115\\tPL:ONT\\tSM:SAMEA7524440 -I1G -a GCA_922984935.2.subset.unmasked.mmi -",
+                    "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.23.1\tCL:samtools sort -@ 3 -o PAE35587_pass_1f1f0707_115.subset.fastq.gz.0.SAMEA7524440.PAE35587.bam -T PAE35587_pass_1f1f0707_115.subset.fastq.gz.0.SAMEA7524440.PAE35587_sort_tmp --write-index -l1 -",
+                    "@PG\tID:samtools.1\tPN:samtools\tPP:samtools\tVN:1.23.1\tCL:samtools merge --threads 3 -c -p --reference GCA_922984935.2.subset.unmasked.fa SAMEA7524440.PAE35587.merge.bam 1/PAE35587_pass_1f1f0707_115.subset.fastq.gz.0.SAMEA7524440.PAE35587.bam",
+                    "@PG\tID:samtools.2\tPN:samtools\tPP:samtools.1\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.ont.SAMEA7524440.PAE35587.minimap2.bam"
+                ],
+                "GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939248.minimap2.bam": [
+                    "@HD\tVN:1.6\tSO:coordinate",
+                    "@SQ\tSN:OV277441.1\tLN:7999920\tM5:0457acf8690429f1c98ee545cb8573b8\tUR:/nfs/treeoflife-01/resources/<ABS_PATH>\tAS:GCA_922984935.2\tAN:SUPER_1\tSP:Meles meles",
+                    "@RG\tID:61ddc6c3/15--15\tPL:PACBIO\tDS:READTYPE=CCS;BINDINGKIT=101-789-500;SEQUENCINGKIT=101-826-100;BASECALLERVERSION=5.0.0;FRAMERATEHZ=100.000000;BarcodeFile=/lustre/scratch116/vr/projects/vgp/ref/barcodes/Sequel_16_Barcodes_v3.fasta;BarcodeHash=e418d89cefcbef90f3cb0e6455b7e2a3;BarcodeCount=16;BarcodeMode=Symmetric;BarcodeQuality=Score\tLB:DN615654G-A1\tPU:m64094_200910_173211\tPM:SEQUELII\tBC:CACTCACGTGTGATATT\tCM:S/P4-C2/5.0-8M\tSM:SAMEA7524440",
+                    "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t4 -ax map-hifi --cs=short -y -R @RG\\tID:61ddc6c3/15--15\\tPL:PACBIO\\tDS:READTYPE=CCS;BINDINGKIT=101-789-500;SEQUENCINGKIT=101-826-100;BASECALLERVERSION=5.0.0;FRAMERATEHZ=100.000000;BarcodeFile=/lustre/scratch116/vr/projects/vgp/ref/barcodes/Sequel_16_Barcodes_v3.fasta;BarcodeHash=e418d89cefcbef90f3cb0e6455b7e2a3;BarcodeCount=16;BarcodeMode=Symmetric;BarcodeQuality=Score\\tLB:DN615654G-A1\\tPU:m64094_200910_173211\\tPM:SEQUELII\\tBC:CACTCACGTGTGATATT\\tCM:S/P4-C2/5.0-8M\\tSM:SAMEA7524440 -I1G -a GCA_922984935.2.subset.unmasked.mmi -",
+                    "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.23.1\tCL:samtools sort -@ 3 -o SAMEA7524440.ERR6939248_other.fastq.gz.0.SAMEA7524440.ERR6939248.bam -T SAMEA7524440.ERR6939248_other.fastq.gz.0.SAMEA7524440.ERR6939248_sort_tmp --write-index -l1 -",
+                    "@PG\tID:samtools.1\tPN:samtools\tPP:samtools\tVN:1.23.1\tCL:samtools merge --threads 3 -c -p --reference GCA_922984935.2.subset.unmasked.fa SAMEA7524440.ERR6939248.merge.bam 1/SAMEA7524440.ERR6939248_other.fastq.gz.0.SAMEA7524440.ERR6939248.bam",
+                    "@PG\tID:crumble\tPN:crumble\tPP:samtools.1\tVN:0.9.1\tCL:crumble -y pbccs -O bam SAMEA7524440.ERR6939248.merge.bam SAMEA7524440.ERR6939248.merge.crumble.bam",
+                    "@PG\tID:samtools.2\tPN:samtools\tPP:crumble\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939248.minimap2.bam"
+                ],
+                "GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.bam": [
+                    "@HD\tVN:1.6\tSO:coordinate",
+                    "@SQ\tSN:OV277441.1\tLN:7999920\tM5:0457acf8690429f1c98ee545cb8573b8\tUR:/nfs/treeoflife-01/resources/<ABS_PATH>\tAS:GCA_922984935.2\tAN:SUPER_1\tSP:Meles meles",
+                    "@RG\tID:m64094_200911_174739\tPL:PACBIO\tSM:SAMEA7524440",
+                    "@PG\tID:samtools.extra_header\tPN:samtools\tVN:1.22.1\tCL:samtools collate --output-fmt cram -O -u -T mMelMel3_T4.collate --threads 4 --reference GCA_922984935.2.subset.unmasked.fasta m64094_200911_174739.ccs.bc1022_BAK8B_OA--bc1022_BAK8B_OA.subset.fastq.gz -",
+                    "@PG\tID:samtools.1.extra_header\tPN:samtools\tPP:samtools\tVN:1.22.1\tCL:samtools fixmate -m -u --threads 4 - -",
+                    "@PG\tID:samtools.2.extra_header\tPN:samtools\tPP:samtools.1\tVN:1.22.1\tCL:samtools sort -u -T mMelMel3_T4.sort --threads 4 -",
+                    "@PG\tID:samtools.3.extra_header\tPN:samtools\tPP:samtools.2\tVN:1.22.1\tCL:samtools markdup -T mMelMel3_T4.markdup -f mMelMel3_T4.metrics --threads 4 - mMelMel3_T4.cram",
+                    "@PG\tID:samtools.4.extra_header\tPN:samtools\tPP:samtools.3\tVN:1.23.1\tCL:samtools view -H m64094_200911_174739.ccs.bc1022_BAK8B_OA--bc1022_BAK8B_OA.subset.cram",
+                    "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t4 -ax map-hifi --cs=short -y -R @RG\\tID:m64094_200911_174739\\tPL:PACBIO\\tSM:SAMEA7524440 -I1G -a GCA_922984935.2.subset.unmasked.mmi -",
+                    "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.23.1\tCL:samtools sort -@ 3 -o m64094_200911_174739.ccs.bc1022_BAK8B_OA--bc1022_BAK8B_OA.subset.fastq.gz.0.SAMEA7524440.ERR6939249.bam -T m64094_200911_174739.ccs.bc1022_BAK8B_OA--bc1022_BAK8B_OA.subset.fastq.gz.0.SAMEA7524440.ERR6939249_sort_tmp --write-index -l1 -",
+                    "@PG\tID:samtools.1\tPN:samtools\tPP:samtools\tVN:1.23.1\tCL:samtools merge --threads 3 -c -p --reference GCA_922984935.2.subset.unmasked.fa SAMEA7524440.ERR6939249.merge.bam 1/m64094_200911_174739.ccs.bc1022_BAK8B_OA--bc1022_BAK8B_OA.subset.fastq.gz.0.SAMEA7524440.ERR6939249.bam",
+                    "@PG\tID:crumble\tPN:crumble\tPP:samtools.1\tVN:0.9.1\tCL:crumble -y pbccs -O bam SAMEA7524440.ERR6939249.merge.bam SAMEA7524440.ERR6939249.merge.crumble.bam",
+                    "@PG\tID:samtools.2\tPN:samtools\tPP:samtools.1.extra_header\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.bam",
+                    "@PG\tID:samtools.3\tPN:samtools\tPP:samtools.2.extra_header\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.bam",
+                    "@PG\tID:samtools.4\tPN:samtools\tPP:crumble\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.bam",
+                    "@PG\tID:samtools.5\tPN:samtools\tPP:samtools.3.extra_header\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.bam",
+                    "@PG\tID:samtools.6\tPN:samtools\tPP:samtools.4.extra_header\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.bam",
+                    "@PG\tID:samtools.7\tPN:samtools\tPP:samtools.4\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.bam"
+                ],
+                "GCA_922984935.2.subset.pacbio.SAMEA7524440.merged_1.minimap2.bam": [
+                    "@HD\tVN:1.6\tSO:coordinate",
+                    "@SQ\tSN:OV277441.1\tLN:7999920\tM5:0457acf8690429f1c98ee545cb8573b8\tUR:/nfs/treeoflife-01/resources/<ABS_PATH>\tAS:GCA_922984935.2\tAN:SUPER_1\tSP:Meles meles",
+                    "@RG\tID:m64094_200911_174739\tPL:PACBIO\tSM:SAMEA7524440",
+                    "@RG\tID:61ddc6c3/15--15\tPL:PACBIO\tDS:READTYPE=CCS;BINDINGKIT=101-789-500;SEQUENCINGKIT=101-826-100;BASECALLERVERSION=5.0.0;FRAMERATEHZ=100.000000;BarcodeFile=/lustre/scratch116/vr/projects/vgp/ref/barcodes/Sequel_16_Barcodes_v3.fasta;BarcodeHash=e418d89cefcbef90f3cb0e6455b7e2a3;BarcodeCount=16;BarcodeMode=Symmetric;BarcodeQuality=Score\tLB:DN615654G-A1\tPU:m64094_200910_173211\tPM:SEQUELII\tBC:CACTCACGTGTGATATT\tCM:S/P4-C2/5.0-8M\tSM:SAMEA7524440",
+                    "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t4 -ax map-hifi --cs=short -y -R @RG\\tID:m64094_200911_174739\\tPL:PACBIO\\tSM:SAMEA7524440 -I1G -a GCA_922984935.2.subset.unmasked.mmi -",
+                    "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.23.1\tCL:samtools sort -@ 3 -o m64094_200911_174739.ccs.bc1022_BAK8B_OA--bc1022_BAK8B_OA.subset.fastq.gz.0.SAMEA7524440.ERR6939249.bam -T m64094_200911_174739.ccs.bc1022_BAK8B_OA--bc1022_BAK8B_OA.subset.fastq.gz.0.SAMEA7524440.ERR6939249_sort_tmp --write-index -l1 -",
+                    "@PG\tID:samtools.1\tPN:samtools\tPP:samtools\tVN:1.23.1\tCL:samtools merge --threads 3 -c -p --reference GCA_922984935.2.subset.unmasked.fa SAMEA7524440.ERR6939249.merge.bam 1/m64094_200911_174739.ccs.bc1022_BAK8B_OA--bc1022_BAK8B_OA.subset.fastq.gz.0.SAMEA7524440.ERR6939249.bam",
+                    "@PG\tID:samtools.2\tPN:samtools\tPP:samtools.1\tVN:1.23.1\tCL:samtools merge --threads 3 -c -p SAMEA7524440.merged_1.merge.bam 1/SAMEA7524440.ERR6939249.merge.bam 2/SAMEA7524440.ERR6939248.merge.bam",
+                    "@PG\tID:crumble\tPN:crumble\tPP:samtools.2\tVN:0.9.1\tCL:crumble -y pbccs -O bam SAMEA7524440.merged_1.merge.bam SAMEA7524440.merged_1.merge.crumble.bam",
+                    "@PG\tID:samtools.3\tPN:samtools\tPP:crumble\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.merged_1.minimap2.bam"
+                ]
+            },
+            {
+                
             },
             [
-
+                
             ]
         ],
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.10.4"
         },
-        "timestamp": "2026-04-29T19:28:07.623617833"
+        "timestamp": "2026-05-29T01:47:41.430447254"
     }
-}
+}
\ No newline at end of file

From 84e057fbc540c5a1ad4daa6c67ee671666d86373 Mon Sep 17 00:00:00 2001
From: sainsachiko <hthhanh.work@gmail.com>
Date: Fri, 29 May 2026 03:00:46 +0100
Subject: [PATCH 07/20] Fix linting

---
 CHANGELOG.md                              |  1 -
 assets/samplesheet_short_reads.csv        |  2 +-
 docs/usage.md                             | 16 ++++++++--------
 modules.json                              |  2 +-
 subworkflows/local/align_long.nf          |  2 +-
 subworkflows/local/align_short.nf         |  6 +++---
 subworkflows/local/convert_stats.nf       |  2 +-
 subworkflows/local/input_check.nf         |  6 +++---
 subworkflows/local/prepare_read_groups.nf |  4 ++--
 workflows/readmapping.nf                  |  2 +-
 10 files changed, 21 insertions(+), 22 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 349e1ff4..eafbbdad 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,7 +3,6 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-
 ## [[v2.1.0-dev](https://github.com/sanger-tol/readmapping/releases/tag/2.1.0-dev)] - 2.1.0-dev - [release-date]
 
 ### Enhancements & fixes
diff --git a/assets/samplesheet_short_reads.csv b/assets/samplesheet_short_reads.csv
index 9af9dc64..8a466b65 100644
--- a/assets/samplesheet_short_reads.csv
+++ b/assets/samplesheet_short_reads.csv
@@ -1,4 +1,4 @@
-specimen,run,datatype,datafile,library,barcode
+specimen,run,datatype,datafile,library,barcode,extra_header
 SAMEA7524438,ERR6688599,illumina,https://tolit.cog.sanger.ac.uk/test-data/Meles_meles/genomic_data/mMelMel1/illumina/31231_3_1.subset.bam,,
 SAMEA7524439,ERR6688600,illumina,https://tolit.cog.sanger.ac.uk/test-data/Meles_meles/genomic_data/mMelMel2/illumina/31231_4_1.subset.fastq.gz,,
 SAMEA7524440,ERR6688402,hic,https://tolit.cog.sanger.ac.uk/test-data/Meles_meles/genomic_data/mMelMel3/hic/35528_2_1.subset.cram,,,https://tolit.cog.sanger.ac.uk/test-data/Meles_meles/genomic_data/mMelMel3/hic/35528_2_1.subset.header_no_rg.sam
diff --git a/docs/usage.md b/docs/usage.md
index 20ce093c..e11bff39 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -40,14 +40,14 @@ specimen2,run4,pacbio,pacbio1.bam,uli,,headers/pacbio_rg.sam
 specimen3,run5,pacbio,pacbio2.bam,,,
 ```
 
-| Column     | Description                                                                                                                                                                                                                                 |
-| ---------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| `specimen` | Identifier of the specimen. Usually a BioSpecimen accession, i,e. `SAMEA7521529`.                                                                                                                                                           |
-| `run`      | Identifier of the sequencing run. Usually the accession number of the data in INSDC. For example,`ERR9248445` (hic), `ERR9284044` (pacbio).                                                                                                 |
-| `datatype` | Type of sequencing data. Must be one of `hic`, `illumina`, `pacbio`, `pacbio_clr`, or `ont`.                                                                                                                                                |
-| `datafile` | Full path to read data file. Must be `bam`, `cram`, `fastq.gz` or `fq.gz` for `illumina` and `hic`. Must be `bam`, `fastq.gz` or `fq.gz` for `pacbio`, `pacbio_clr`, and `ont`. Note that FASTQ inputs should be interleaved if paired-end. |
-| `library`  | (Optional) The library value is a unique identifier which is assigned to read group (`@RG`) ID. If the library name is not specified, the pipeline will auto-create library name using the data filename provided in the samplesheet.       |
-| `barcode`  | (Optional) Barcode identifier used to trim barcode adapter for PacBio reads. If empty, barcode-specific adapter sequences will not be trimmed.                                                                                              |
+| Column         | Description                                                                                                                                                                                                                                                                            |
+| -------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| `specimen`     | Identifier of the specimen. Usually a BioSpecimen accession, i,e. `SAMEA7521529`.                                                                                                                                                                                                      |
+| `run`          | Identifier of the sequencing run. Usually the accession number of the data in INSDC. For example,`ERR9248445` (hic), `ERR9284044` (pacbio).                                                                                                                                            |
+| `datatype`     | Type of sequencing data. Must be one of `hic`, `illumina`, `pacbio`, `pacbio_clr`, or `ont`.                                                                                                                                                                                           |
+| `datafile`     | Full path to read data file. Must be `bam`, `cram`, `fastq.gz` or `fq.gz` for `illumina` and `hic`. Must be `bam`, `fastq.gz` or `fq.gz` for `pacbio`, `pacbio_clr`, and `ont`. Note that FASTQ inputs should be interleaved if paired-end.                                            |
+| `library`      | (Optional) The library value is a unique identifier which is assigned to read group (`@RG`) ID. If the library name is not specified, the pipeline will auto-create library name using the data filename provided in the samplesheet.                                                  |
+| `barcode`      | (Optional) Barcode identifier used to trim barcode adapter for PacBio reads. If empty, barcode-specific adapter sequences will not be trimmed.                                                                                                                                         |
 | `extra_header` | (Optional) Path to a SAM file containing additional SAM header lines including `@RG`, `@PG`. These information will be injected into output BAM/CRAM headers. `@RG` lines are overwritten, while `@PG` lines are added to the existing headers (auto add `.extra_header` to `@PG ID`). |
 
 An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline.
diff --git a/modules.json b/modules.json
index c00ecfad..979208ba 100644
--- a/modules.json
+++ b/modules.json
@@ -77,7 +77,7 @@
                     },
                     "samtools/addreplacerg": {
                         "branch": "master",
-                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
+                        "git_sha": "156feda0cb6589cd29c04902004fa3b53bc00205",
                         "installed_by": ["modules"]
                     },
                     "samtools/bgzip": {
diff --git a/subworkflows/local/align_long.nf b/subworkflows/local/align_long.nf
index 4982e0d1..cc72428f 100644
--- a/subworkflows/local/align_long.nf
+++ b/subworkflows/local/align_long.nf
@@ -63,7 +63,7 @@ workflow ALIGN_LONG {
             ch_yaml_meta = ch_reads.pacbio
                 .combine( channel.fromPath(val_pacbio_adapter_yaml, checkIfExists: true) )
                 .map{ meta, _reads, yaml -> [ meta, yaml ]}
-                .branch { meta, yaml ->
+                .branch { meta, _yaml ->
                     has_barcode: meta.barcode != null && !meta.barcode.isEmpty()
                     no_barcode: true
                 }
diff --git a/subworkflows/local/align_short.nf b/subworkflows/local/align_short.nf
index 1b91a437..8f285fa2 100644
--- a/subworkflows/local/align_short.nf
+++ b/subworkflows/local/align_short.nf
@@ -22,10 +22,10 @@ workflow ALIGN_SHORT {
     reads_with_rg = PREPARE_READ_GROUPS.out.reads
 
     //
-    // LOGIC: Convert FASTQ to CRAM adn add RG information if needed
+    // LOGIC: Convert FASTQ to CRAM and add RG information if needed
     //
     // Check file types and branch
-    ch_reads = reads_with_rg.branch { meta, read_files ->
+    ch_reads = reads_with_rg.branch { _meta, read_files ->
         cram: read_files.name.endsWith(".cram")
         non_cram: true
     }
@@ -39,7 +39,7 @@ workflow ALIGN_SHORT {
     // Add read group information to CRAMs if not already present, and merge with CRAMs that already have RG information
     ch_crams_to_addrg = CONVERT_CRAM.out.cram
         .mix ( ch_reads.cram )
-        .branch { meta, cram ->
+        .branch { meta, _cram ->
             replace_rg: meta.replace_rg == true
             not_replace_rg: true
         }
diff --git a/subworkflows/local/convert_stats.nf b/subworkflows/local/convert_stats.nf
index e8ad5005..dac085d4 100644
--- a/subworkflows/local/convert_stats.nf
+++ b/subworkflows/local/convert_stats.nf
@@ -96,7 +96,7 @@ workflow CONVERT_STATS {
 
     if ( "bam" in outfmt_options ) {
         // Re-header && reindex BAM
-        ch_bam = params.header ? SAMTOOLS_REHEADER_BAM ( ch_bams_add_pg, header.first() ).bam : ch_bams_add_pg.map{ meta, bam, _empty-> [ meta, bam ] }
+        ch_bam = params.header ? SAMTOOLS_REHEADER_BAM ( ch_bams_add_pg, header.first() ).bam : ch_bams_add_pg.map{ meta, bam_file, _empty -> [ meta, bam_file ] }
         SAMTOOLS_INDEX_BAM ( ch_bam )
 
         // Set the BAM and BAI channels for emission
diff --git a/subworkflows/local/input_check.nf b/subworkflows/local/input_check.nf
index 07be329a..4d7134c5 100644
--- a/subworkflows/local/input_check.nf
+++ b/subworkflows/local/input_check.nf
@@ -22,7 +22,7 @@ workflow INPUT_CHECK {
     SAMTOOLS_FLAGSTAT ( samplesheet_rows )
 
     // Create the read channel for the rest of the pipeline
-    reads = samplesheet_rows
+    ch_reads = samplesheet_rows
     .join( SAMTOOLS_FLAGSTAT.out.flagstat )
     .map { meta, datafile, _meta2, stats -> create_data_channel( meta, datafile, stats ) }
 
@@ -39,7 +39,7 @@ workflow INPUT_CHECK {
     MASK_UNMASK ( ch_fasta_for_unmask )
 
     emit:
-    reads                                        // channel: [ val(meta), /path/to/datafile ]
+    reads    = ch_reads                            // channel: [ val(meta), /path/to/datafile ]
     fasta    = MASK_UNMASK.out.unmasked.first()    // channel: [ meta, /path/to/fasta ]
 }
 
@@ -55,7 +55,7 @@ def create_data_channel ( LinkedHashMap row, datafile, stats ) {
     meta.datatype      = row.datatype
     meta.library       = row.library
     meta.barcode       = row.barcode
-    meta.extra_header  = row.extra_header ? file(row.extra_header, checkExists:true) : []
+    meta.extra_header  = row.extra_header ? file(row.extra_header, checkIfExists: true) : []
 
     def platform = (meta.datatype == "hic" || meta.datatype == "illumina") ? "ILLUMINA" :
                 (meta.datatype == "pacbio" || meta.datatype == "pacbio_clr") ? "PACBIO" :
diff --git a/subworkflows/local/prepare_read_groups.nf b/subworkflows/local/prepare_read_groups.nf
index 04ff501d..8f87f196 100644
--- a/subworkflows/local/prepare_read_groups.nf
+++ b/subworkflows/local/prepare_read_groups.nf
@@ -46,7 +46,7 @@ workflow PREPARE_READ_GROUPS {
                             : "${line}\tSM:${meta.id}"
                     "${rg_flag} '${l.replaceAll("\t", "\\\\t")}'"
                 }.join(' ')
-            ].findAll { it }.join(' ')
+            ].findAll { value -> value }.join(' ')
             : (meta.read_group ?: '')
 
             def output_read_files = meta.read_file ?: read_files
@@ -60,5 +60,5 @@ workflow PREPARE_READ_GROUPS {
         .mix(ch_reads_extra_header.no_extra_header_fastq)
 
     emit:
-    reads = ch_reads_with_rg       // channel: [ val(meta), /path/to/read_file ]
+    reads = ch_reads_with_rg               // channel: [ val(meta), /path/to/read_file ]
 }
diff --git a/workflows/readmapping.nf b/workflows/readmapping.nf
index 50797945..f522562f 100644
--- a/workflows/readmapping.nf
+++ b/workflows/readmapping.nf
@@ -159,7 +159,7 @@ workflow READMAPPING {
 
 
     emit:
-    versions       = ch_collated_versions                 // channel: [ path(versions.yml) ]
+    versions = ch_collated_versions                                  // channel: [ path(versions.yml) ]
 
 }
 

From dc76ec2d6eff04f7df330c46c4ee7f63e5ef5530 Mon Sep 17 00:00:00 2001
From: sainsachiko <hthhanh.work@gmail.com>
Date: Fri, 29 May 2026 03:26:37 +0100
Subject: [PATCH 08/20] fix(samtools-reheader): preserve @PG chain when
 suffixing extra header IDs

---
 .../reheader/samtools_replaceheader.nf        |   3 +-
 tests/default.nf.test.snap                    | 110 ++++++++----------
 tests/short_aligner_minimap2.nf.test.snap     |  68 ++++++++---
 tests/untrim.nf.test.snap                     |  20 ++--
 4 files changed, 112 insertions(+), 89 deletions(-)

diff --git a/modules/local/samtools/reheader/samtools_replaceheader.nf b/modules/local/samtools/reheader/samtools_replaceheader.nf
index fd06babd..93123950 100644
--- a/modules/local/samtools/reheader/samtools_replaceheader.nf
+++ b/modules/local/samtools/reheader/samtools_replaceheader.nf
@@ -24,7 +24,8 @@ process SAMTOOLS_REHEADER {
     suffix = file.getExtension()
     def sq_template = header_template ? " | grep -v ^@SQ && grep '^@SQ' ${header_template}" : ""
     // Suffix all PG IDs from sample extra_header to keep them distinct from native file-header PG IDs.
-    def pg_extra = sample_extra_header ? "grep '^@PG' ${sample_extra_header} | awk 'BEGIN { FS = OFS = \"\\t\" } { for (i = 1; i <= NF; i++) if (\$i ~ /^ID:/) { \$i = \$i \".extra_header\"; break } print }' || true" : "true"
+    // Also rewrite matching PP references so the extra-header PG chain remains intact after suffixing.
+    def pg_extra = sample_extra_header ? "awk 'BEGIN { FS = OFS = \"\\t\" } FNR == NR { if (\$1 == \"@PG\") for (i = 1; i <= NF; i++) if (\$i ~ /^ID:/) { ids[substr(\$i, 4)] = 1; break } next } \$1 == \"@PG\" { for (i = 1; i <= NF; i++) { if (\$i ~ /^ID:/) { \$i = \$i \".extra_header\" } else if (\$i ~ /^PP:/) { pp = substr(\$i, 4); if (pp in ids) \$i = \"PP:\" pp \".extra_header\" } } print }' ${sample_extra_header} ${sample_extra_header} || true" : "true"
 
     if ("$file" == "${prefix}.${suffix}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
     """
diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap
index d33de6ed..13ed1309 100644
--- a/tests/default.nf.test.snap
+++ b/tests/default.nf.test.snap
@@ -389,21 +389,21 @@
                     "@SQ\tSN:OV277441.1\tLN:7999920\tM5:0457acf8690429f1c98ee545cb8573b8\tUR:/nfs/treeoflife-01/<ABS_PATH>\tAS:GCA_922984935.2\tAN:SUPER_1\tSP:Meles meles",
                     "@RG\tID:35528_2_1\tPL:ILLUMINA\tSM:SAMEA7524440",
                     "@PG\tID:SCS.extra_header\tVN:1.7.0\tPN:NovaSeq Control Software\tDS:Controlling software on instrument",
-                    "@PG\tID:basecalling.extra_header\tPP:SCS\tVN:Unknown\tPN:Unknown\tDS:Basecalling Package",
-                    "@PG\tID:bambi.extra_header\tPP:basecalling\tVN:0.13.1\tCL:/software/pkgg/bambi/0.13.1/bin/bambi i2b --intensity-dir=/lustre/scratch121/esa-sv-20200210-01/IL_seq_data/analysis/201117_A00948_0206_AHGML2DSXY/Data/Intensities --basecalls-dir=/lustre/scratch121/esa-sv-20200210-01/IL_seq_data/analysis/201117_A00948_0206_AHGML2DSXY/Data/Intensities/BaseCalls --lane=2 --platform-unit=201117_A00948_0206_AHGML2DSXY_2 --read-group-id=35528_2 --study-name=\"ERP116890: Sequencing and assembly of genomes from British species for the Darwin Tree of Life Project. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ \" --sample-alias=SAMEA5962964,mCerEla1 --threads=8 --output-file=- --compression-level=0\tPN:bambi\tDS:Convert Illumina BCL to BAM or SAM file",
-                    "@PG\tID:bambi.1.extra_header\tPN:bambi\tPP:bambi\tVN:0.13.1\tCL:/software/pkgg/bambi/0.13.1/bin/bambi decode --metrics-file /lustre/scratch121/esa-sv-20200210-01/IL_seq_data/analysis/201117_A00948_0206_AHGML2DSXY/Data/Intensities/BAM_basecalls_20201119-090808/35528_2.bam.tag_decode.metrics --barcode-file /lustre/scratch121/esa-sv-20200210-01/IL_seq_data/analysis/201117_A00948_0206_AHGML2DSXY/Data/Intensities/BAM_basecalls_20201119-090808/metadata_cache_35528/lane_2.taglist --compression-level 0 -",
-                    "@PG\tID:bamcollate2.extra_header\tPN:bamcollate2\tCL:/software/pkgg/biobambam2/2.0.79/bin/bamcollate2 collate=2 level=0\tPP:bambi.1\tVN:2.0.79",
-                    "@PG\tID:minimap2.extra_header\tPN:minimap2\tCL:minimap2 -ax sr --MD -t 3 -Y -F 1200 -K 100000000 /lustre/scratch121/npg_repository/references/PhiX/Sanger-SNPs/all/minimap2/phix_unsnipped_short_no_N.fa.mmi /tmp/wr_cwd/0/e/8/dce75fe12433429e1b439b8872bc7693328371/tmp/s0uOqe6xfG/alnphix_bamtofastq_out\tPP:bamcollate2\tVN:2.10-r761",
-                    "@PG\tID:samtools.extra_header\tPN:samtools\tCL:/software/pkgg/samtools/1.11.0/bin/samtools view --threads 3 -u -F 0x900 -\tPP:minimap2\tVN:1.11",
-                    "@PG\tID:bam12auxmerge.extra_header\tPN:bam12auxmerge\tCL:/software/pkgg/biobambam2/2.0.79/bin/bam12auxmerge level=0 rankstrip=1 ranksplit=1 zztoname=0 clipreinsert=1 /tmp/wr_cwd/0/e/8/dce75fe12433429e1b439b8872bc7693328371/tmp/ac_8ARdDJl/tee_collated:td1_out\tPP:samtools\tVN:2.0.79",
-                    "@PG\tID:samtools.1.extra_header\tPN:samtools\tPP:bam12auxmerge\tVN:1.11\tCL:/software/pkgg/samtools/1.11.0/bin/samtools split --threads 4 --output-fmt cram,no_ref=1 -f /lustre/scratch121/esa-sv-20200210-01/IL_seq_data/analysis/201117_A00948_0206_AHGML2DSXY/Data/Intensities/BAM_basecalls_20201119-090808/no_cal/%!.cram -",
-                    "@PG\tID:samtools.2.extra_header\tPN:samtools\tPP:samtools.1\tVN:1.11\tCL:/software/pkgg/samtools/1.11.0/bin/samtools merge -n -O BAM -l 0 --input-fmt-option no_ref=1 - /lustre/scratch121/esa-sv-20200210-01/IL_seq_data/analysis/201117_A00948_0206_AHGML2DSXY/Data/Intensities/BAM_basecalls_20201119-090808/no_cal/35528_2#1.cram",
-                    "@PG\tID:spf.extra_header\tPN:spatial_filter\tPP:samtools.2\tDS:A program to apply a spatial filter\tVN:0.13.1\tCL:/software/pkgg/bambi/0.13.1/bin/bambi spatial_filter -a --compression-level 0 -f -l /lustre/scratch121/esa-sv-20200210-01/IL_seq_data/analysis/201117_A00948_0206_AHGML2DSXY/Data/Intensities/BAM_basecalls_20201119-090808/no_cal/archive/lane2/plex1/35528_2#1.spatial_filter.stats -F /lustre/scratch121/esa-sv-20200210-01/IL_seq_data/analysis/201117_A00948_0206_AHGML2DSXY/Data/Intensities/BAM_basecalls_20201119-090808/no_cal/35528_2.spatial_filter --rg 35528_2#1 -",
-                    "@PG\tID:bambi.2.extra_header\tPN:bambi\tPP:spf\tVN:0.13.1\tCL:/software/pkgg/bambi/0.13.1/bin/bambi select --compression-level 0 --input /tmp/wr_cwd/5/0/6/86a8369ba62bab2227fd63e2ff1ad119662395/tmp/9RE_mnwwls/ssfqc_tee_ssfqc:straight_through1_out --output /tmp/wr_cwd/5/0/6/86a8369ba62bab2227fd63e2ff1ad119662395/tmp/b6x1p8j3v_/alignment_filter:phix_bam_out_out -n /tmp/wr_cwd/5/0/6/86a8369ba62bab2227fd63e2ff1ad119662395/tmp/IuuBniSlRB/alignment_filter:target_bam_out_out -m 35528_2#1_bam_alignment_filter_metrics.json\tDS:Split alignments into different files",
-                    "@PG\tID:scramble.extra_header\tPN:scramble\tPP:bambi.2\tVN:1.14.9\tCL:/software/pkgg/io_lib/1.14.9/bin/scramble -t 5 -7 -I bam -O cram -x ",
-                    "@PG\tID:samtools.3.extra_header\tPN:samtools\tPP:scramble\tVN:1.15\tCL:/usr/local/bin/samtools view -h /lustre/scratch124/tol/projects/darwin/data/mammals/Meles_meles/genomic_data/mMelMel3/hic-arima2/35528_2#1.cram",
-                    "@PG\tID:samtools.4.extra_header\tPN:samtools\tPP:samtools.3\tVN:1.20\tCL:/usr/local/bin/samtools view --cram 35528_2#1.subset.sam",
-                    "@PG\tID:samtools.5.extra_header\tPN:samtools\tPP:samtools.4\tVN:1.23.1\tCL:samtools view -H 35528_2_1.subset.cram",
+                    "@PG\tID:basecalling.extra_header\tPP:SCS.extra_header\tVN:Unknown\tPN:Unknown\tDS:Basecalling Package",
+                    "@PG\tID:bambi.extra_header\tPP:basecalling.extra_header\tVN:0.13.1\tCL:/software/pkgg/bambi/0.13.1/bin/bambi i2b --intensity-dir=/lustre/scratch121/esa-sv-20200210-01/IL_seq_data/analysis/201117_A00948_0206_AHGML2DSXY/Data/Intensities --basecalls-dir=/lustre/scratch121/esa-sv-20200210-01/IL_seq_data/analysis/201117_A00948_0206_AHGML2DSXY/Data/Intensities/BaseCalls --lane=2 --platform-unit=201117_A00948_0206_AHGML2DSXY_2 --read-group-id=35528_2 --study-name=\"ERP116890: Sequencing and assembly of genomes from British species for the Darwin Tree of Life Project. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ \" --sample-alias=SAMEA5962964,mCerEla1 --threads=8 --output-file=- --compression-level=0\tPN:bambi\tDS:Convert Illumina BCL to BAM or SAM file",
+                    "@PG\tID:bambi.1.extra_header\tPN:bambi\tPP:bambi.extra_header\tVN:0.13.1\tCL:/software/pkgg/bambi/0.13.1/bin/bambi decode --metrics-file /lustre/scratch121/esa-sv-20200210-01/IL_seq_data/analysis/201117_A00948_0206_AHGML2DSXY/Data/Intensities/BAM_basecalls_20201119-090808/35528_2.bam.tag_decode.metrics --barcode-file /lustre/scratch121/esa-sv-20200210-01/IL_seq_data/analysis/201117_A00948_0206_AHGML2DSXY/Data/Intensities/BAM_basecalls_20201119-090808/metadata_cache_35528/lane_2.taglist --compression-level 0 -",
+                    "@PG\tID:bamcollate2.extra_header\tPN:bamcollate2\tCL:/software/pkgg/biobambam2/2.0.79/bin/bamcollate2 collate=2 level=0\tPP:bambi.1.extra_header\tVN:2.0.79",
+                    "@PG\tID:minimap2.extra_header\tPN:minimap2\tCL:minimap2 -ax sr --MD -t 3 -Y -F 1200 -K 100000000 /lustre/scratch121/npg_repository/references/PhiX/Sanger-SNPs/all/minimap2/phix_unsnipped_short_no_N.fa.mmi /tmp/wr_cwd/0/e/8/dce75fe12433429e1b439b8872bc7693328371/tmp/s0uOqe6xfG/alnphix_bamtofastq_out\tPP:bamcollate2.extra_header\tVN:2.10-r761",
+                    "@PG\tID:samtools.extra_header\tPN:samtools\tCL:/software/pkgg/samtools/1.11.0/bin/samtools view --threads 3 -u -F 0x900 -\tPP:minimap2.extra_header\tVN:1.11",
+                    "@PG\tID:bam12auxmerge.extra_header\tPN:bam12auxmerge\tCL:/software/pkgg/biobambam2/2.0.79/bin/bam12auxmerge level=0 rankstrip=1 ranksplit=1 zztoname=0 clipreinsert=1 /tmp/wr_cwd/0/e/8/dce75fe12433429e1b439b8872bc7693328371/tmp/ac_8ARdDJl/tee_collated:td1_out\tPP:samtools.extra_header\tVN:2.0.79",
+                    "@PG\tID:samtools.1.extra_header\tPN:samtools\tPP:bam12auxmerge.extra_header\tVN:1.11\tCL:/software/pkgg/samtools/1.11.0/bin/samtools split --threads 4 --output-fmt cram,no_ref=1 -f /lustre/scratch121/esa-sv-20200210-01/IL_seq_data/analysis/201117_A00948_0206_AHGML2DSXY/Data/Intensities/BAM_basecalls_20201119-090808/no_cal/%!.cram -",
+                    "@PG\tID:samtools.2.extra_header\tPN:samtools\tPP:samtools.1.extra_header\tVN:1.11\tCL:/software/pkgg/samtools/1.11.0/bin/samtools merge -n -O BAM -l 0 --input-fmt-option no_ref=1 - /lustre/scratch121/esa-sv-20200210-01/IL_seq_data/analysis/201117_A00948_0206_AHGML2DSXY/Data/Intensities/BAM_basecalls_20201119-090808/no_cal/35528_2#1.cram",
+                    "@PG\tID:spf.extra_header\tPN:spatial_filter\tPP:samtools.2.extra_header\tDS:A program to apply a spatial filter\tVN:0.13.1\tCL:/software/pkgg/bambi/0.13.1/bin/bambi spatial_filter -a --compression-level 0 -f -l /lustre/scratch121/esa-sv-20200210-01/IL_seq_data/analysis/201117_A00948_0206_AHGML2DSXY/Data/Intensities/BAM_basecalls_20201119-090808/no_cal/archive/lane2/plex1/35528_2#1.spatial_filter.stats -F /lustre/scratch121/esa-sv-20200210-01/IL_seq_data/analysis/201117_A00948_0206_AHGML2DSXY/Data/Intensities/BAM_basecalls_20201119-090808/no_cal/35528_2.spatial_filter --rg 35528_2#1 -",
+                    "@PG\tID:bambi.2.extra_header\tPN:bambi\tPP:spf.extra_header\tVN:0.13.1\tCL:/software/pkgg/bambi/0.13.1/bin/bambi select --compression-level 0 --input /tmp/wr_cwd/5/0/6/86a8369ba62bab2227fd63e2ff1ad119662395/tmp/9RE_mnwwls/ssfqc_tee_ssfqc:straight_through1_out --output /tmp/wr_cwd/5/0/6/86a8369ba62bab2227fd63e2ff1ad119662395/tmp/b6x1p8j3v_/alignment_filter:phix_bam_out_out -n /tmp/wr_cwd/5/0/6/86a8369ba62bab2227fd63e2ff1ad119662395/tmp/IuuBniSlRB/alignment_filter:target_bam_out_out -m 35528_2#1_bam_alignment_filter_metrics.json\tDS:Split alignments into different files",
+                    "@PG\tID:scramble.extra_header\tPN:scramble\tPP:bambi.2.extra_header\tVN:1.14.9\tCL:/software/pkgg/io_lib/1.14.9/bin/scramble -t 5 -7 -I bam -O cram -x ",
+                    "@PG\tID:samtools.3.extra_header\tPN:samtools\tPP:scramble.extra_header\tVN:1.15\tCL:/usr/local/bin/samtools view -h /lustre/scratch124/tol/projects/darwin/data/mammals/Meles_meles/genomic_data/mMelMel3/hic-arima2/35528_2#1.cram",
+                    "@PG\tID:samtools.4.extra_header\tPN:samtools\tPP:samtools.3.extra_header\tVN:1.20\tCL:/usr/local/bin/samtools view --cram 35528_2#1.subset.sam",
+                    "@PG\tID:samtools.5.extra_header\tPN:samtools\tPP:samtools.4.extra_header\tVN:1.23.1\tCL:samtools view -H 35528_2_1.subset.cram",
                     "@PG\tID:bwa-mem2\tPN:bwa-mem2\tVN:2.2.1\tCL:bwa-mem2 mem -5SPCp -t 4 ./bwamem2/GCA_922984935.2.subset.unmasked.fa -C -H @RG\\tID:35528_2_1\\tPL:ILLUMINA\\tSM:SAMEA7524440 -",
                     "@PG\tID:samtools\tPN:samtools\tPP:bwa-mem2\tVN:1.22.1\tCL:samtools fixmate -mpu - -",
                     "@PG\tID:samtools.1\tPN:samtools\tPP:samtools\tVN:1.22.1\tCL:samtools view -h",
@@ -411,24 +411,12 @@
                     "@PG\tID:samtools.3\tPN:samtools\tPP:samtools.2\tVN:1.23.1\tCL:samtools merge --threads 3 -c -p --reference GCA_922984935.2.subset.unmasked.fa - 1/35528_2_1.subset_addRG.cram.0.SAMEA7524440.ERR6688402.bam 2/35528_2_1.subset_addRG.cram.1.SAMEA7524440.ERR6688402.bam",
                     "@PG\tID:samtools.4\tPN:samtools\tPP:samtools.3\tVN:1.23.1\tCL:samtools markdup -T SAMEA7524440.ERR6688402 -f SAMEA7524440.ERR6688402.metrics --threads 4 --reference GCA_922984935.2.subset.unmasked.fa - SAMEA7524440.ERR6688402.bam",
                     "@PG\tID:crumble\tPN:crumble\tPP:samtools.4\tVN:0.9.1\tCL:crumble -O bam SAMEA7524440.ERR6688402.bam SAMEA7524440.ERR6688402.crumble.bam",
-                    "@PG\tID:samtools.5\tPN:samtools\tPP:bam12auxmerge.extra_header\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.bwamem2.bam",
-                    "@PG\tID:samtools.6\tPN:samtools\tPP:samtools.2.extra_header\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.bwamem2.bam",
-                    "@PG\tID:samtools.7\tPN:samtools\tPP:spf.extra_header\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.bwamem2.bam",
-                    "@PG\tID:samtools.8\tPN:samtools\tPP:samtools.4.extra_header\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.bwamem2.bam",
-                    "@PG\tID:samtools.9\tPN:samtools\tPP:samtools.5.extra_header\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.bwamem2.bam",
-                    "@PG\tID:samtools.10\tPN:samtools\tPP:crumble\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.bwamem2.bam",
-                    "@PG\tID:samtools.11\tPN:samtools\tPP:samtools.5\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1,lossy_names=1 --write-index -o GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.bwamem2.cram GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.bwamem2.bam",
-                    "@PG\tID:samtools.12\tPN:samtools\tPP:samtools.6\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1,lossy_names=1 --write-index -o GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.bwamem2.cram GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.bwamem2.bam",
-                    "@PG\tID:samtools.13\tPN:samtools\tPP:samtools.7\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1,lossy_names=1 --write-index -o GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.bwamem2.cram GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.bwamem2.bam",
-                    "@PG\tID:samtools.14\tPN:samtools\tPP:samtools.8\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1,lossy_names=1 --write-index -o GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.bwamem2.cram GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.bwamem2.bam",
-                    "@PG\tID:samtools.15\tPN:samtools\tPP:samtools.9\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1,lossy_names=1 --write-index -o GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.bwamem2.cram GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.bwamem2.bam",
-                    "@PG\tID:samtools.16\tPN:samtools\tPP:samtools.10\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1,lossy_names=1 --write-index -o GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.bwamem2.cram GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.bwamem2.bam",
-                    "@PG\tID:samtools.17\tPN:samtools\tPP:samtools.11\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.bwamem2.cram",
-                    "@PG\tID:samtools.18\tPN:samtools\tPP:samtools.12\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.bwamem2.cram",
-                    "@PG\tID:samtools.19\tPN:samtools\tPP:samtools.13\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.bwamem2.cram",
-                    "@PG\tID:samtools.20\tPN:samtools\tPP:samtools.14\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.bwamem2.cram",
-                    "@PG\tID:samtools.21\tPN:samtools\tPP:samtools.15\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.bwamem2.cram",
-                    "@PG\tID:samtools.22\tPN:samtools\tPP:samtools.16\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.bwamem2.cram"
+                    "@PG\tID:samtools.5\tPN:samtools\tPP:samtools.5.extra_header\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.bwamem2.bam",
+                    "@PG\tID:samtools.6\tPN:samtools\tPP:crumble\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.bwamem2.bam",
+                    "@PG\tID:samtools.7\tPN:samtools\tPP:samtools.5\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1,lossy_names=1 --write-index -o GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.bwamem2.cram GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.bwamem2.bam",
+                    "@PG\tID:samtools.8\tPN:samtools\tPP:samtools.6\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1,lossy_names=1 --write-index -o GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.bwamem2.cram GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.bwamem2.bam",
+                    "@PG\tID:samtools.9\tPN:samtools\tPP:samtools.7\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.bwamem2.cram",
+                    "@PG\tID:samtools.10\tPN:samtools\tPP:samtools.8\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.bwamem2.cram"
                 ],
                 "GCA_922984935.2.subset.illumina.SAMEA7524438.ERR6688599.bwamem2.cram": [
                     "@HD\tVN:1.6\tSO:coordinate",
@@ -481,11 +469,11 @@
                 "GCA_922984935.2.subset.ont.SAMEA7524440.merged_1.minimap2.cram": [
                     "@HD\tVN:1.6\tSO:coordinate",
                     "@SQ\tSN:OV277441.1\tLN:7999920\tM5:0457acf8690429f1c98ee545cb8573b8\tUR:/nfs/treeoflife-01/<ABS_PATH>\tAS:GCA_922984935.2\tAN:SUPER_1\tSP:Meles meles",
-                    "@RG\tID:PAE35587_pass_1f1f0707_115\tPL:ONT\tSM:mMelMel3",
-                    "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t4 -ax map-ont -y -R @RG\\tID:PAE35587_pass_1f1f0707_115\\tPL:ONT\\tSM:mMelMel3 -I1G -a GCA_922984935.2.subset.unmasked.mmi -",
-                    "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.23.1\tCL:samtools sort -@ 3 -o SAMEA7524440.PAE35587_test_other.fastq.gz.0.SAMEA7524440.PAE35587_test.bam -T SAMEA7524440.PAE35587_test_other.fastq.gz.0.SAMEA7524440.PAE35587_test_sort_tmp --write-index -l1 -",
-                    "@PG\tID:samtools.1\tPN:samtools\tPP:samtools\tVN:1.23.1\tCL:samtools merge --threads 3 -c -p --reference GCA_922984935.2.subset.unmasked.fa SAMEA7524440.PAE35587_test.merge.bam 1/SAMEA7524440.PAE35587_test_other.fastq.gz.0.SAMEA7524440.PAE35587_test.bam",
-                    "@PG\tID:samtools.2\tPN:samtools\tPP:samtools.1\tVN:1.23.1\tCL:samtools merge --threads 3 -c -p SAMEA7524440.merged_1.merge.bam 1/SAMEA7524440.PAE35587_test.merge.bam 2/SAMEA7524440.PAE35587.merge.bam",
+                    "@RG\tID:PAE35587_pass_1f1f0707_115\tPL:ONT\tSM:SAMEA7524440",
+                    "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t4 -ax map-ont -y -R @RG\\tID:PAE35587_pass_1f1f0707_115\\tPL:ONT\\tSM:SAMEA7524440 -I1G -a GCA_922984935.2.subset.unmasked.mmi -",
+                    "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.23.1\tCL:samtools sort -@ 3 -o PAE35587_pass_1f1f0707_115.subset.fastq.gz.0.SAMEA7524440.PAE35587.bam -T PAE35587_pass_1f1f0707_115.subset.fastq.gz.0.SAMEA7524440.PAE35587_sort_tmp --write-index -l1 -",
+                    "@PG\tID:samtools.1\tPN:samtools\tPP:samtools\tVN:1.23.1\tCL:samtools merge --threads 3 -c -p --reference GCA_922984935.2.subset.unmasked.fa SAMEA7524440.PAE35587.merge.bam 1/PAE35587_pass_1f1f0707_115.subset.fastq.gz.0.SAMEA7524440.PAE35587.bam",
+                    "@PG\tID:samtools.2\tPN:samtools\tPP:samtools.1\tVN:1.23.1\tCL:samtools merge --threads 3 -c -p SAMEA7524440.merged_1.merge.bam 1/SAMEA7524440.PAE35587.merge.bam 2/SAMEA7524440.PAE35587_test.merge.bam",
                     "@PG\tID:samtools.3\tPN:samtools\tPP:samtools.2\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1 --write-index -o GCA_922984935.2.subset.ont.SAMEA7524440.merged_1.minimap2.cram GCA_922984935.2.subset.ont.SAMEA7524440.merged_1.minimap2.bam",
                     "@PG\tID:samtools.4\tPN:samtools\tPP:samtools.3\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.ont.SAMEA7524440.merged_1.minimap2.cram"
                 ],
@@ -495,45 +483,39 @@
                     "@RG\tID:61ddc6c3/15--15\tPL:PACBIO\tDS:READTYPE=CCS;BINDINGKIT=101-789-500;SEQUENCINGKIT=101-826-100;BASECALLERVERSION=5.0.0;FRAMERATEHZ=100.000000;BarcodeFile=/lustre/scratch116/vr/projects/vgp/ref/barcodes/Sequel_16_Barcodes_v3.fasta;BarcodeHash=e418d89cefcbef90f3cb0e6455b7e2a3;BarcodeCount=16;BarcodeMode=Symmetric;BarcodeQuality=Score\tLB:DN615654G-A1\tPU:m64094_200910_173211\tPM:SEQUELII\tBC:CACTCACGTGTGATATT\tCM:S/P4-C2/5.0-8M\tSM:SAMEA7524440",
                     "@PG\tID:ccs-4.2.0.extra_header\tPN:ccs\tVN:4.2.0\tDS:Generate circular consensus sequences (ccs) from subreads.\tCL:ccs ccs --chunk 1/64 -j 8 --max-length 50000 ../../m64094_200910_173211.subreads.bam m64094_200910_173211.ccs.bam",
                     "@PG\tID:lima.extra_header\tVN:1.11.0 (commit v1.11.0)\tCL:lima -j 8 --split-bam-named --same --peek-guess --guess-min-count 1000 --ccs m64094_200910_173211.ccs.bam /lustre/scratch116/vr/projects/vgp/ref/barcodes/Sequel_16_Barcodes_v3.fasta lima/m64094_200910_173211.ccs.bam",
-                    "@PG\tID:samtools.extra_header\tPN:samtools\tVN:1.10\tPP:ccs-4.2.0\tCL:samtools merge -@8 -ncp -b m64094_200910_173211.chunks.fofn m64094_200910_173211.ccs.bam",
-                    "@PG\tID:samtools.1.extra_header\tPN:samtools\tPP:samtools\tVN:1.19.2\tCL:samtools view -b -h -N /nfs/users/nfs_m/mm49/READS -o /nfs/users/nfs_m/mm49/x.bam m64094_200910_173211.ccs.bc1022_BAK8B_OA--bc1022_BAK8B_OA.bam",
-                    "@PG\tID:samtools.2.extra_header\tPN:samtools\tPP:samtools.1\tVN:1.23.1\tCL:samtools view -H m64094_200910_173211.ccs.bc1022_BAK8B_OA--bc1022_BAK8B_OA.subset.bam",
+                    "@PG\tID:samtools.extra_header\tPN:samtools\tVN:1.10\tPP:ccs-4.2.0.extra_header\tCL:samtools merge -@8 -ncp -b m64094_200910_173211.chunks.fofn m64094_200910_173211.ccs.bam",
+                    "@PG\tID:samtools.1.extra_header\tPN:samtools\tPP:samtools.extra_header\tVN:1.19.2\tCL:samtools view -b -h -N /nfs/users/nfs_m/mm49/READS -o /nfs/users/nfs_m/mm49/x.bam m64094_200910_173211.ccs.bc1022_BAK8B_OA--bc1022_BAK8B_OA.bam",
+                    "@PG\tID:samtools.2.extra_header\tPN:samtools\tPP:samtools.1.extra_header\tVN:1.23.1\tCL:samtools view -H m64094_200910_173211.ccs.bc1022_BAK8B_OA--bc1022_BAK8B_OA.subset.bam",
                     "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t4 -ax map-hifi --cs=short -y -R @RG\\tID:61ddc6c3/15--15\\tPL:PACBIO\\tDS:READTYPE=CCS;BINDINGKIT=101-789-500;SEQUENCINGKIT=101-826-100;BASECALLERVERSION=5.0.0;FRAMERATEHZ=100.000000;BarcodeFile=/lustre/scratch116/vr/projects/vgp/ref/barcodes/Sequel_16_Barcodes_v3.fasta;BarcodeHash=e418d89cefcbef90f3cb0e6455b7e2a3;BarcodeCount=16;BarcodeMode=Symmetric;BarcodeQuality=Score\\tLB:DN615654G-A1\\tPU:m64094_200910_173211\\tPM:SEQUELII\\tBC:CACTCACGTGTGATATT\\tCM:S/P4-C2/5.0-8M\\tSM:SAMEA7524440 -I1G -a GCA_922984935.2.subset.unmasked.mmi -",
                     "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.23.1\tCL:samtools sort -@ 3 -o pacbio.SAMEA7524440.ERR6939248.hifitrimmer.fastq.gz.0.SAMEA7524440.ERR6939248.bam -T pacbio.SAMEA7524440.ERR6939248.hifitrimmer.fastq.gz.0.SAMEA7524440.ERR6939248_sort_tmp --write-index -l1 -",
                     "@PG\tID:samtools.1\tPN:samtools\tPP:samtools\tVN:1.23.1\tCL:samtools merge --threads 3 -c -p --reference GCA_922984935.2.subset.unmasked.fa SAMEA7524440.ERR6939248.merge.bam 1/pacbio.SAMEA7524440.ERR6939248.hifitrimmer.fastq.gz.0.SAMEA7524440.ERR6939248.bam",
                     "@PG\tID:crumble\tPN:crumble\tPP:samtools.1\tVN:0.9.1\tCL:crumble -y pbccs -O bam SAMEA7524440.ERR6939248.merge.bam SAMEA7524440.ERR6939248.merge.crumble.bam",
-                    "@PG\tID:samtools.2\tPN:samtools\tPP:samtools.1.extra_header\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939248.minimap2.bam",
-                    "@PG\tID:samtools.3\tPN:samtools\tPP:samtools.2.extra_header\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939248.minimap2.bam",
-                    "@PG\tID:samtools.4\tPN:samtools\tPP:crumble\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939248.minimap2.bam",
-                    "@PG\tID:samtools.5\tPN:samtools\tPP:samtools.2\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1 --write-index -o GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939248.minimap2.cram GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939248.minimap2.bam",
-                    "@PG\tID:samtools.6\tPN:samtools\tPP:samtools.3\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1 --write-index -o GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939248.minimap2.cram GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939248.minimap2.bam",
-                    "@PG\tID:samtools.7\tPN:samtools\tPP:samtools.4\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1 --write-index -o GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939248.minimap2.cram GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939248.minimap2.bam",
-                    "@PG\tID:samtools.8\tPN:samtools\tPP:samtools.5\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939248.minimap2.cram",
-                    "@PG\tID:samtools.9\tPN:samtools\tPP:samtools.6\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939248.minimap2.cram",
-                    "@PG\tID:samtools.10\tPN:samtools\tPP:samtools.7\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939248.minimap2.cram"
+                    "@PG\tID:samtools.2\tPN:samtools\tPP:samtools.2.extra_header\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939248.minimap2.bam",
+                    "@PG\tID:samtools.3\tPN:samtools\tPP:crumble\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939248.minimap2.bam",
+                    "@PG\tID:samtools.4\tPN:samtools\tPP:samtools.2\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1 --write-index -o GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939248.minimap2.cram GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939248.minimap2.bam",
+                    "@PG\tID:samtools.5\tPN:samtools\tPP:samtools.3\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1 --write-index -o GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939248.minimap2.cram GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939248.minimap2.bam",
+                    "@PG\tID:samtools.6\tPN:samtools\tPP:samtools.4\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939248.minimap2.cram",
+                    "@PG\tID:samtools.7\tPN:samtools\tPP:samtools.5\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939248.minimap2.cram"
                 ],
                 "GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.cram": [
                     "@HD\tVN:1.6\tSO:coordinate",
                     "@SQ\tSN:OV277441.1\tLN:7999920\tM5:0457acf8690429f1c98ee545cb8573b8\tUR:/nfs/treeoflife-01/<ABS_PATH>\tAS:GCA_922984935.2\tAN:SUPER_1\tSP:Meles meles",
                     "@RG\tID:m64094_200911_174739\tPL:PACBIO\tSM:SAMEA7524440",
                     "@PG\tID:samtools.extra_header\tPN:samtools\tVN:1.22.1\tCL:samtools collate --output-fmt cram -O -u -T mMelMel3_T4.collate --threads 4 --reference GCA_922984935.2.subset.unmasked.fasta m64094_200911_174739.ccs.bc1022_BAK8B_OA--bc1022_BAK8B_OA.subset.fastq.gz -",
-                    "@PG\tID:samtools.1.extra_header\tPN:samtools\tPP:samtools\tVN:1.22.1\tCL:samtools fixmate -m -u --threads 4 - -",
-                    "@PG\tID:samtools.2.extra_header\tPN:samtools\tPP:samtools.1\tVN:1.22.1\tCL:samtools sort -u -T mMelMel3_T4.sort --threads 4 -",
-                    "@PG\tID:samtools.3.extra_header\tPN:samtools\tPP:samtools.2\tVN:1.22.1\tCL:samtools markdup -T mMelMel3_T4.markdup -f mMelMel3_T4.metrics --threads 4 - mMelMel3_T4.cram",
-                    "@PG\tID:samtools.4.extra_header\tPN:samtools\tPP:samtools.3\tVN:1.23.1\tCL:samtools view -H m64094_200911_174739.ccs.bc1022_BAK8B_OA--bc1022_BAK8B_OA.subset.cram",
+                    "@PG\tID:samtools.1.extra_header\tPN:samtools\tPP:samtools.extra_header\tVN:1.22.1\tCL:samtools fixmate -m -u --threads 4 - -",
+                    "@PG\tID:samtools.2.extra_header\tPN:samtools\tPP:samtools.1.extra_header\tVN:1.22.1\tCL:samtools sort -u -T mMelMel3_T4.sort --threads 4 -",
+                    "@PG\tID:samtools.3.extra_header\tPN:samtools\tPP:samtools.2.extra_header\tVN:1.22.1\tCL:samtools markdup -T mMelMel3_T4.markdup -f mMelMel3_T4.metrics --threads 4 - mMelMel3_T4.cram",
+                    "@PG\tID:samtools.4.extra_header\tPN:samtools\tPP:samtools.3.extra_header\tVN:1.23.1\tCL:samtools view -H m64094_200911_174739.ccs.bc1022_BAK8B_OA--bc1022_BAK8B_OA.subset.cram",
                     "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t4 -ax map-hifi --cs=short -y -R @RG\\tID:m64094_200911_174739\\tPL:PACBIO\\tSM:SAMEA7524440 -I1G -a GCA_922984935.2.subset.unmasked.mmi -",
                     "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.23.1\tCL:samtools sort -@ 3 -o pacbio.SAMEA7524440.ERR6939249.hifitrimmer.fastq.gz.0.SAMEA7524440.ERR6939249.bam -T pacbio.SAMEA7524440.ERR6939249.hifitrimmer.fastq.gz.0.SAMEA7524440.ERR6939249_sort_tmp --write-index -l1 -",
                     "@PG\tID:samtools.1\tPN:samtools\tPP:samtools\tVN:1.23.1\tCL:samtools merge --threads 3 -c -p --reference GCA_922984935.2.subset.unmasked.fa SAMEA7524440.ERR6939249.merge.bam 1/pacbio.SAMEA7524440.ERR6939249.hifitrimmer.fastq.gz.0.SAMEA7524440.ERR6939249.bam",
                     "@PG\tID:crumble\tPN:crumble\tPP:samtools.1\tVN:0.9.1\tCL:crumble -y pbccs -O bam SAMEA7524440.ERR6939249.merge.bam SAMEA7524440.ERR6939249.merge.crumble.bam",
-                    "@PG\tID:samtools.2\tPN:samtools\tPP:samtools.1.extra_header\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.bam",
-                    "@PG\tID:samtools.3\tPN:samtools\tPP:samtools.2.extra_header\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.bam",
-                    "@PG\tID:samtools.4\tPN:samtools\tPP:crumble\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.bam",
-                    "@PG\tID:samtools.5\tPN:samtools\tPP:samtools.3.extra_header\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1 --write-index -o GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.cram GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.bam",
-                    "@PG\tID:samtools.6\tPN:samtools\tPP:samtools.4.extra_header\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1 --write-index -o GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.cram GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.bam",
-                    "@PG\tID:samtools.7\tPN:samtools\tPP:samtools.4\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1 --write-index -o GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.cram GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.bam",
-                    "@PG\tID:samtools.8\tPN:samtools\tPP:samtools.5\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.cram",
-                    "@PG\tID:samtools.9\tPN:samtools\tPP:samtools.6\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.cram",
-                    "@PG\tID:samtools.10\tPN:samtools\tPP:samtools.7\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.cram"
+                    "@PG\tID:samtools.2\tPN:samtools\tPP:samtools.4.extra_header\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.bam",
+                    "@PG\tID:samtools.3\tPN:samtools\tPP:crumble\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.bam",
+                    "@PG\tID:samtools.4\tPN:samtools\tPP:samtools.2\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1 --write-index -o GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.cram GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.bam",
+                    "@PG\tID:samtools.5\tPN:samtools\tPP:samtools.3\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1 --write-index -o GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.cram GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.bam",
+                    "@PG\tID:samtools.6\tPN:samtools\tPP:samtools.4\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.cram",
+                    "@PG\tID:samtools.7\tPN:samtools\tPP:samtools.5\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.cram"
                 ],
                 "GCA_922984935.2.subset.pacbio.SAMEA7524440.merged_1.minimap2.cram": [
                     "@HD\tVN:1.6\tSO:coordinate",
@@ -558,6 +540,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.4"
         },
-        "timestamp": "2026-05-29T01:57:02.637423352"
+        "timestamp": "2026-05-29T03:22:38.8477332"
     }
 }
\ No newline at end of file
diff --git a/tests/short_aligner_minimap2.nf.test.snap b/tests/short_aligner_minimap2.nf.test.snap
index c48be2e6..8926f46d 100644
--- a/tests/short_aligner_minimap2.nf.test.snap
+++ b/tests/short_aligner_minimap2.nf.test.snap
@@ -1,7 +1,7 @@
 {
     "-profile test --short_aligner minimap2 --outfmt 'bam,cram'": {
         "content": [
-            79,
+            81,
             {
                 "BGZIP_BEDGRAPH": {
                     "samtools": "1.23.1"
@@ -46,6 +46,9 @@
                 "SAMTOOLS_ADDREPLACERG": {
                     "samtools": "1.23.1"
                 },
+                "SAMTOOLS_ADD_PG": {
+                    "samtools": "1.23.1"
+                },
                 "SAMTOOLS_CRAM": {
                     "samtools": "1.23.1"
                 },
@@ -224,15 +227,34 @@
                 "GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.minimap2.bam": [
                     "@HD\tVN:1.6\tSO:coordinate",
                     "@SQ\tSN:OV277441.1\tLN:7999920\tM5:0457acf8690429f1c98ee545cb8573b8\tUR:/nfs/treeoflife-01/<ABS_PATH>\tAS:GCA_922984935.2\tAN:SUPER_1\tSP:Meles meles",
-                    "@RG\tID:35528_2#1\tDT:2020-11-17T00:00:00+0000\tPU:201117_A00948_0206_AHGML2DSXY_2#1\tLB:33637906\tPG:SCS\tSM:SAMEA5962964\tCN:SC\tPL:ILLUMINA\tDS:ERP116890: Sequencing and assembly of genomes from British species for the Darwin Tree of Life Project. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ ",
-                    "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t4 -ax sr --cs=short -I1.0G -y -R @RG\\tID:35528_2#1\\tDT:2020-11-17T00:00:00+0000\\tPU:201117_A00948_0206_AHGML2DSXY_2#1\\tLB:33637906\\tPG:SCS\\tSM:SAMEA5962964\\tCN:SC\\tPL:ILLUMINA\\tDS:ERP116890: Sequencing and assembly of genomes from British species for the Darwin Tree of Life Project. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/  GCA_922984935.2.subset.unmasked.mmi -",
+                    "@RG\tID:35528_2_1\tPL:ILLUMINA\tSM:SAMEA7524440",
+                    "@PG\tID:SCS.extra_header\tVN:1.7.0\tPN:NovaSeq Control Software\tDS:Controlling software on instrument",
+                    "@PG\tID:basecalling.extra_header\tPP:SCS.extra_header\tVN:Unknown\tPN:Unknown\tDS:Basecalling Package",
+                    "@PG\tID:bambi.extra_header\tPP:basecalling.extra_header\tVN:0.13.1\tCL:/software/pkgg/bambi/0.13.1/bin/bambi i2b --intensity-dir=/lustre/scratch121/esa-sv-20200210-01/IL_seq_data/analysis/201117_A00948_0206_AHGML2DSXY/Data/Intensities --basecalls-dir=/lustre/scratch121/esa-sv-20200210-01/IL_seq_data/analysis/201117_A00948_0206_AHGML2DSXY/Data/Intensities/BaseCalls --lane=2 --platform-unit=201117_A00948_0206_AHGML2DSXY_2 --read-group-id=35528_2 --study-name=\"ERP116890: Sequencing and assembly of genomes from British species for the Darwin Tree of Life Project. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ \" --sample-alias=SAMEA5962964,mCerEla1 --threads=8 --output-file=- --compression-level=0\tPN:bambi\tDS:Convert Illumina BCL to BAM or SAM file",
+                    "@PG\tID:bambi.1.extra_header\tPN:bambi\tPP:bambi.extra_header\tVN:0.13.1\tCL:/software/pkgg/bambi/0.13.1/bin/bambi decode --metrics-file /lustre/scratch121/esa-sv-20200210-01/IL_seq_data/analysis/201117_A00948_0206_AHGML2DSXY/Data/Intensities/BAM_basecalls_20201119-090808/35528_2.bam.tag_decode.metrics --barcode-file /lustre/scratch121/esa-sv-20200210-01/IL_seq_data/analysis/201117_A00948_0206_AHGML2DSXY/Data/Intensities/BAM_basecalls_20201119-090808/metadata_cache_35528/lane_2.taglist --compression-level 0 -",
+                    "@PG\tID:bamcollate2.extra_header\tPN:bamcollate2\tCL:/software/pkgg/biobambam2/2.0.79/bin/bamcollate2 collate=2 level=0\tPP:bambi.1.extra_header\tVN:2.0.79",
+                    "@PG\tID:minimap2.extra_header\tPN:minimap2\tCL:minimap2 -ax sr --MD -t 3 -Y -F 1200 -K 100000000 /lustre/scratch121/npg_repository/references/PhiX/Sanger-SNPs/all/minimap2/phix_unsnipped_short_no_N.fa.mmi /tmp/wr_cwd/0/e/8/dce75fe12433429e1b439b8872bc7693328371/tmp/s0uOqe6xfG/alnphix_bamtofastq_out\tPP:bamcollate2.extra_header\tVN:2.10-r761",
+                    "@PG\tID:samtools.extra_header\tPN:samtools\tCL:/software/pkgg/samtools/1.11.0/bin/samtools view --threads 3 -u -F 0x900 -\tPP:minimap2.extra_header\tVN:1.11",
+                    "@PG\tID:bam12auxmerge.extra_header\tPN:bam12auxmerge\tCL:/software/pkgg/biobambam2/2.0.79/bin/bam12auxmerge level=0 rankstrip=1 ranksplit=1 zztoname=0 clipreinsert=1 /tmp/wr_cwd/0/e/8/dce75fe12433429e1b439b8872bc7693328371/tmp/ac_8ARdDJl/tee_collated:td1_out\tPP:samtools.extra_header\tVN:2.0.79",
+                    "@PG\tID:samtools.1.extra_header\tPN:samtools\tPP:bam12auxmerge.extra_header\tVN:1.11\tCL:/software/pkgg/samtools/1.11.0/bin/samtools split --threads 4 --output-fmt cram,no_ref=1 -f /lustre/scratch121/esa-sv-20200210-01/IL_seq_data/analysis/201117_A00948_0206_AHGML2DSXY/Data/Intensities/BAM_basecalls_20201119-090808/no_cal/%!.cram -",
+                    "@PG\tID:samtools.2.extra_header\tPN:samtools\tPP:samtools.1.extra_header\tVN:1.11\tCL:/software/pkgg/samtools/1.11.0/bin/samtools merge -n -O BAM -l 0 --input-fmt-option no_ref=1 - /lustre/scratch121/esa-sv-20200210-01/IL_seq_data/analysis/201117_A00948_0206_AHGML2DSXY/Data/Intensities/BAM_basecalls_20201119-090808/no_cal/35528_2#1.cram",
+                    "@PG\tID:spf.extra_header\tPN:spatial_filter\tPP:samtools.2.extra_header\tDS:A program to apply a spatial filter\tVN:0.13.1\tCL:/software/pkgg/bambi/0.13.1/bin/bambi spatial_filter -a --compression-level 0 -f -l /lustre/scratch121/esa-sv-20200210-01/IL_seq_data/analysis/201117_A00948_0206_AHGML2DSXY/Data/Intensities/BAM_basecalls_20201119-090808/no_cal/archive/lane2/plex1/35528_2#1.spatial_filter.stats -F /lustre/scratch121/esa-sv-20200210-01/IL_seq_data/analysis/201117_A00948_0206_AHGML2DSXY/Data/Intensities/BAM_basecalls_20201119-090808/no_cal/35528_2.spatial_filter --rg 35528_2#1 -",
+                    "@PG\tID:bambi.2.extra_header\tPN:bambi\tPP:spf.extra_header\tVN:0.13.1\tCL:/software/pkgg/bambi/0.13.1/bin/bambi select --compression-level 0 --input /tmp/wr_cwd/5/0/6/86a8369ba62bab2227fd63e2ff1ad119662395/tmp/9RE_mnwwls/ssfqc_tee_ssfqc:straight_through1_out --output /tmp/wr_cwd/5/0/6/86a8369ba62bab2227fd63e2ff1ad119662395/tmp/b6x1p8j3v_/alignment_filter:phix_bam_out_out -n /tmp/wr_cwd/5/0/6/86a8369ba62bab2227fd63e2ff1ad119662395/tmp/IuuBniSlRB/alignment_filter:target_bam_out_out -m 35528_2#1_bam_alignment_filter_metrics.json\tDS:Split alignments into different files",
+                    "@PG\tID:scramble.extra_header\tPN:scramble\tPP:bambi.2.extra_header\tVN:1.14.9\tCL:/software/pkgg/io_lib/1.14.9/bin/scramble -t 5 -7 -I bam -O cram -x ",
+                    "@PG\tID:samtools.3.extra_header\tPN:samtools\tPP:scramble.extra_header\tVN:1.15\tCL:/usr/local/bin/samtools view -h /lustre/scratch124/tol/projects/darwin/data/mammals/Meles_meles/genomic_data/mMelMel3/hic-arima2/35528_2#1.cram",
+                    "@PG\tID:samtools.4.extra_header\tPN:samtools\tPP:samtools.3.extra_header\tVN:1.20\tCL:/usr/local/bin/samtools view --cram 35528_2#1.subset.sam",
+                    "@PG\tID:samtools.5.extra_header\tPN:samtools\tPP:samtools.4.extra_header\tVN:1.23.1\tCL:samtools view -H 35528_2_1.subset.cram",
+                    "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t4 -ax sr --cs=short -I1.0G -y -R @RG\\tID:35528_2_1\\tPL:ILLUMINA\\tSM:SAMEA7524440 GCA_922984935.2.subset.unmasked.mmi -",
                     "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.22.1\tCL:samtools fixmate -mpu - -",
                     "@PG\tID:samtools.1\tPN:samtools\tPP:samtools\tVN:1.22.1\tCL:samtools view -h",
-                    "@PG\tID:samtools.2\tPN:samtools\tPP:samtools.1\tVN:1.22.1\tCL:samtools sort --write-index -l1 -@4 -T 35528_2_1.subset.cram.0.SAMEA7524440.ERR6688402_tmp -o 35528_2_1.subset.cram.0.SAMEA7524440.ERR6688402.bam -",
-                    "@PG\tID:samtools.3\tPN:samtools\tPP:samtools.2\tVN:1.23.1\tCL:samtools merge --threads 3 -c -p --reference GCA_922984935.2.subset.unmasked.fa - 1/35528_2_1.subset.cram.0.SAMEA7524440.ERR6688402.bam 2/35528_2_1.subset.cram.1.SAMEA7524440.ERR6688402.bam",
+                    "@PG\tID:samtools.2\tPN:samtools\tPP:samtools.1\tVN:1.22.1\tCL:samtools sort --write-index -l1 -@4 -T 35528_2_1.subset_addRG.cram.0.SAMEA7524440.ERR6688402_tmp -o 35528_2_1.subset_addRG.cram.0.SAMEA7524440.ERR6688402.bam -",
+                    "@PG\tID:samtools.3\tPN:samtools\tPP:samtools.2\tVN:1.23.1\tCL:samtools merge --threads 3 -c -p --reference GCA_922984935.2.subset.unmasked.fa - 1/35528_2_1.subset_addRG.cram.0.SAMEA7524440.ERR6688402.bam 2/35528_2_1.subset_addRG.cram.1.SAMEA7524440.ERR6688402.bam",
                     "@PG\tID:samtools.4\tPN:samtools\tPP:samtools.3\tVN:1.23.1\tCL:samtools markdup -T SAMEA7524440.ERR6688402 -f SAMEA7524440.ERR6688402.metrics --threads 4 --reference GCA_922984935.2.subset.unmasked.fa - SAMEA7524440.ERR6688402.bam",
                     "@PG\tID:crumble\tPN:crumble\tPP:samtools.4\tVN:0.9.1\tCL:crumble -O bam SAMEA7524440.ERR6688402.bam SAMEA7524440.ERR6688402.crumble.bam",
-                    "@PG\tID:samtools.5\tPN:samtools\tPP:crumble\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.minimap2.bam"
+                    "@PG\tID:samtools.5\tPN:samtools\tPP:samtools.5.extra_header\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.minimap2.bam",
+                    "@PG\tID:samtools.6\tPN:samtools\tPP:crumble\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.minimap2.bam",
+                    "@PG\tID:samtools.7\tPN:samtools\tPP:samtools.5\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.minimap2.bam",
+                    "@PG\tID:samtools.8\tPN:samtools\tPP:samtools.6\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.minimap2.bam"
                 ],
                 "GCA_922984935.2.subset.illumina.SAMEA7524438.ERR6688599.minimap2.bam": [
                     "@HD\tVN:1.6\tSO:coordinate",
@@ -265,16 +287,36 @@
                 "GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.minimap2.cram": [
                     "@HD\tVN:1.6\tSO:coordinate",
                     "@SQ\tSN:OV277441.1\tLN:7999920\tM5:0457acf8690429f1c98ee545cb8573b8\tUR:/nfs/treeoflife-01/<ABS_PATH>\tAS:GCA_922984935.2\tAN:SUPER_1\tSP:Meles meles",
-                    "@RG\tID:35528_2#1\tDT:2020-11-17T00:00:00+0000\tPU:201117_A00948_0206_AHGML2DSXY_2#1\tLB:33637906\tPG:SCS\tSM:SAMEA5962964\tCN:SC\tPL:ILLUMINA\tDS:ERP116890: Sequencing and assembly of genomes from British species for the Darwin Tree of Life Project. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ ",
-                    "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t4 -ax sr --cs=short -I1.0G -y -R @RG\\tID:35528_2#1\\tDT:2020-11-17T00:00:00+0000\\tPU:201117_A00948_0206_AHGML2DSXY_2#1\\tLB:33637906\\tPG:SCS\\tSM:SAMEA5962964\\tCN:SC\\tPL:ILLUMINA\\tDS:ERP116890: Sequencing and assembly of genomes from British species for the Darwin Tree of Life Project. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/  GCA_922984935.2.subset.unmasked.mmi -",
+                    "@RG\tID:35528_2_1\tPL:ILLUMINA\tSM:SAMEA7524440",
+                    "@PG\tID:SCS.extra_header\tVN:1.7.0\tPN:NovaSeq Control Software\tDS:Controlling software on instrument",
+                    "@PG\tID:basecalling.extra_header\tPP:SCS.extra_header\tVN:Unknown\tPN:Unknown\tDS:Basecalling Package",
+                    "@PG\tID:bambi.extra_header\tPP:basecalling.extra_header\tVN:0.13.1\tCL:/software/pkgg/bambi/0.13.1/bin/bambi i2b --intensity-dir=/lustre/scratch121/esa-sv-20200210-01/IL_seq_data/analysis/201117_A00948_0206_AHGML2DSXY/Data/Intensities --basecalls-dir=/lustre/scratch121/esa-sv-20200210-01/IL_seq_data/analysis/201117_A00948_0206_AHGML2DSXY/Data/Intensities/BaseCalls --lane=2 --platform-unit=201117_A00948_0206_AHGML2DSXY_2 --read-group-id=35528_2 --study-name=\"ERP116890: Sequencing and assembly of genomes from British species for the Darwin Tree of Life Project. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ \" --sample-alias=SAMEA5962964,mCerEla1 --threads=8 --output-file=- --compression-level=0\tPN:bambi\tDS:Convert Illumina BCL to BAM or SAM file",
+                    "@PG\tID:bambi.1.extra_header\tPN:bambi\tPP:bambi.extra_header\tVN:0.13.1\tCL:/software/pkgg/bambi/0.13.1/bin/bambi decode --metrics-file /lustre/scratch121/esa-sv-20200210-01/IL_seq_data/analysis/201117_A00948_0206_AHGML2DSXY/Data/Intensities/BAM_basecalls_20201119-090808/35528_2.bam.tag_decode.metrics --barcode-file /lustre/scratch121/esa-sv-20200210-01/IL_seq_data/analysis/201117_A00948_0206_AHGML2DSXY/Data/Intensities/BAM_basecalls_20201119-090808/metadata_cache_35528/lane_2.taglist --compression-level 0 -",
+                    "@PG\tID:bamcollate2.extra_header\tPN:bamcollate2\tCL:/software/pkgg/biobambam2/2.0.79/bin/bamcollate2 collate=2 level=0\tPP:bambi.1.extra_header\tVN:2.0.79",
+                    "@PG\tID:minimap2.extra_header\tPN:minimap2\tCL:minimap2 -ax sr --MD -t 3 -Y -F 1200 -K 100000000 /lustre/scratch121/npg_repository/references/PhiX/Sanger-SNPs/all/minimap2/phix_unsnipped_short_no_N.fa.mmi /tmp/wr_cwd/0/e/8/dce75fe12433429e1b439b8872bc7693328371/tmp/s0uOqe6xfG/alnphix_bamtofastq_out\tPP:bamcollate2.extra_header\tVN:2.10-r761",
+                    "@PG\tID:samtools.extra_header\tPN:samtools\tCL:/software/pkgg/samtools/1.11.0/bin/samtools view --threads 3 -u -F 0x900 -\tPP:minimap2.extra_header\tVN:1.11",
+                    "@PG\tID:bam12auxmerge.extra_header\tPN:bam12auxmerge\tCL:/software/pkgg/biobambam2/2.0.79/bin/bam12auxmerge level=0 rankstrip=1 ranksplit=1 zztoname=0 clipreinsert=1 /tmp/wr_cwd/0/e/8/dce75fe12433429e1b439b8872bc7693328371/tmp/ac_8ARdDJl/tee_collated:td1_out\tPP:samtools.extra_header\tVN:2.0.79",
+                    "@PG\tID:samtools.1.extra_header\tPN:samtools\tPP:bam12auxmerge.extra_header\tVN:1.11\tCL:/software/pkgg/samtools/1.11.0/bin/samtools split --threads 4 --output-fmt cram,no_ref=1 -f /lustre/scratch121/esa-sv-20200210-01/IL_seq_data/analysis/201117_A00948_0206_AHGML2DSXY/Data/Intensities/BAM_basecalls_20201119-090808/no_cal/%!.cram -",
+                    "@PG\tID:samtools.2.extra_header\tPN:samtools\tPP:samtools.1.extra_header\tVN:1.11\tCL:/software/pkgg/samtools/1.11.0/bin/samtools merge -n -O BAM -l 0 --input-fmt-option no_ref=1 - /lustre/scratch121/esa-sv-20200210-01/IL_seq_data/analysis/201117_A00948_0206_AHGML2DSXY/Data/Intensities/BAM_basecalls_20201119-090808/no_cal/35528_2#1.cram",
+                    "@PG\tID:spf.extra_header\tPN:spatial_filter\tPP:samtools.2.extra_header\tDS:A program to apply a spatial filter\tVN:0.13.1\tCL:/software/pkgg/bambi/0.13.1/bin/bambi spatial_filter -a --compression-level 0 -f -l /lustre/scratch121/esa-sv-20200210-01/IL_seq_data/analysis/201117_A00948_0206_AHGML2DSXY/Data/Intensities/BAM_basecalls_20201119-090808/no_cal/archive/lane2/plex1/35528_2#1.spatial_filter.stats -F /lustre/scratch121/esa-sv-20200210-01/IL_seq_data/analysis/201117_A00948_0206_AHGML2DSXY/Data/Intensities/BAM_basecalls_20201119-090808/no_cal/35528_2.spatial_filter --rg 35528_2#1 -",
+                    "@PG\tID:bambi.2.extra_header\tPN:bambi\tPP:spf.extra_header\tVN:0.13.1\tCL:/software/pkgg/bambi/0.13.1/bin/bambi select --compression-level 0 --input /tmp/wr_cwd/5/0/6/86a8369ba62bab2227fd63e2ff1ad119662395/tmp/9RE_mnwwls/ssfqc_tee_ssfqc:straight_through1_out --output /tmp/wr_cwd/5/0/6/86a8369ba62bab2227fd63e2ff1ad119662395/tmp/b6x1p8j3v_/alignment_filter:phix_bam_out_out -n /tmp/wr_cwd/5/0/6/86a8369ba62bab2227fd63e2ff1ad119662395/tmp/IuuBniSlRB/alignment_filter:target_bam_out_out -m 35528_2#1_bam_alignment_filter_metrics.json\tDS:Split alignments into different files",
+                    "@PG\tID:scramble.extra_header\tPN:scramble\tPP:bambi.2.extra_header\tVN:1.14.9\tCL:/software/pkgg/io_lib/1.14.9/bin/scramble -t 5 -7 -I bam -O cram -x ",
+                    "@PG\tID:samtools.3.extra_header\tPN:samtools\tPP:scramble.extra_header\tVN:1.15\tCL:/usr/local/bin/samtools view -h /lustre/scratch124/tol/projects/darwin/data/mammals/Meles_meles/genomic_data/mMelMel3/hic-arima2/35528_2#1.cram",
+                    "@PG\tID:samtools.4.extra_header\tPN:samtools\tPP:samtools.3.extra_header\tVN:1.20\tCL:/usr/local/bin/samtools view --cram 35528_2#1.subset.sam",
+                    "@PG\tID:samtools.5.extra_header\tPN:samtools\tPP:samtools.4.extra_header\tVN:1.23.1\tCL:samtools view -H 35528_2_1.subset.cram",
+                    "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t4 -ax sr --cs=short -I1.0G -y -R @RG\\tID:35528_2_1\\tPL:ILLUMINA\\tSM:SAMEA7524440 GCA_922984935.2.subset.unmasked.mmi -",
                     "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.22.1\tCL:samtools fixmate -mpu - -",
                     "@PG\tID:samtools.1\tPN:samtools\tPP:samtools\tVN:1.22.1\tCL:samtools view -h",
-                    "@PG\tID:samtools.2\tPN:samtools\tPP:samtools.1\tVN:1.22.1\tCL:samtools sort --write-index -l1 -@4 -T 35528_2_1.subset.cram.0.SAMEA7524440.ERR6688402_tmp -o 35528_2_1.subset.cram.0.SAMEA7524440.ERR6688402.bam -",
-                    "@PG\tID:samtools.3\tPN:samtools\tPP:samtools.2\tVN:1.23.1\tCL:samtools merge --threads 3 -c -p --reference GCA_922984935.2.subset.unmasked.fa - 1/35528_2_1.subset.cram.0.SAMEA7524440.ERR6688402.bam 2/35528_2_1.subset.cram.1.SAMEA7524440.ERR6688402.bam",
+                    "@PG\tID:samtools.2\tPN:samtools\tPP:samtools.1\tVN:1.22.1\tCL:samtools sort --write-index -l1 -@4 -T 35528_2_1.subset_addRG.cram.0.SAMEA7524440.ERR6688402_tmp -o 35528_2_1.subset_addRG.cram.0.SAMEA7524440.ERR6688402.bam -",
+                    "@PG\tID:samtools.3\tPN:samtools\tPP:samtools.2\tVN:1.23.1\tCL:samtools merge --threads 3 -c -p --reference GCA_922984935.2.subset.unmasked.fa - 1/35528_2_1.subset_addRG.cram.0.SAMEA7524440.ERR6688402.bam 2/35528_2_1.subset_addRG.cram.1.SAMEA7524440.ERR6688402.bam",
                     "@PG\tID:samtools.4\tPN:samtools\tPP:samtools.3\tVN:1.23.1\tCL:samtools markdup -T SAMEA7524440.ERR6688402 -f SAMEA7524440.ERR6688402.metrics --threads 4 --reference GCA_922984935.2.subset.unmasked.fa - SAMEA7524440.ERR6688402.bam",
                     "@PG\tID:crumble\tPN:crumble\tPP:samtools.4\tVN:0.9.1\tCL:crumble -O bam SAMEA7524440.ERR6688402.bam SAMEA7524440.ERR6688402.crumble.bam",
-                    "@PG\tID:samtools.5\tPN:samtools\tPP:crumble\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1,lossy_names=1 --write-index -o GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.minimap2.cram GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.minimap2.bam",
-                    "@PG\tID:samtools.6\tPN:samtools\tPP:samtools.5\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.minimap2.cram"
+                    "@PG\tID:samtools.5\tPN:samtools\tPP:samtools.5.extra_header\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.minimap2.bam",
+                    "@PG\tID:samtools.6\tPN:samtools\tPP:crumble\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.minimap2.bam",
+                    "@PG\tID:samtools.7\tPN:samtools\tPP:samtools.5\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1,lossy_names=1 --write-index -o GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.minimap2.cram GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.minimap2.bam",
+                    "@PG\tID:samtools.8\tPN:samtools\tPP:samtools.6\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1,lossy_names=1 --write-index -o GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.minimap2.cram GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.minimap2.bam",
+                    "@PG\tID:samtools.9\tPN:samtools\tPP:samtools.7\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.minimap2.cram",
+                    "@PG\tID:samtools.10\tPN:samtools\tPP:samtools.8\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.minimap2.cram"
                 ],
                 "GCA_922984935.2.subset.illumina.SAMEA7524438.ERR6688599.minimap2.cram": [
                     "@HD\tVN:1.6\tSO:coordinate",
@@ -313,6 +355,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.4"
         },
-        "timestamp": "2026-05-29T01:22:33.94399251"
+        "timestamp": "2026-05-29T03:07:26.580580159"
     }
 }
\ No newline at end of file
diff --git a/tests/untrim.nf.test.snap b/tests/untrim.nf.test.snap
index 5ebff3c9..1b98a7cb 100644
--- a/tests/untrim.nf.test.snap
+++ b/tests/untrim.nf.test.snap
@@ -222,20 +222,18 @@
                     "@SQ\tSN:OV277441.1\tLN:7999920\tM5:0457acf8690429f1c98ee545cb8573b8\tUR:/nfs/treeoflife-01/resources/<ABS_PATH>\tAS:GCA_922984935.2\tAN:SUPER_1\tSP:Meles meles",
                     "@RG\tID:m64094_200911_174739\tPL:PACBIO\tSM:SAMEA7524440",
                     "@PG\tID:samtools.extra_header\tPN:samtools\tVN:1.22.1\tCL:samtools collate --output-fmt cram -O -u -T mMelMel3_T4.collate --threads 4 --reference GCA_922984935.2.subset.unmasked.fasta m64094_200911_174739.ccs.bc1022_BAK8B_OA--bc1022_BAK8B_OA.subset.fastq.gz -",
-                    "@PG\tID:samtools.1.extra_header\tPN:samtools\tPP:samtools\tVN:1.22.1\tCL:samtools fixmate -m -u --threads 4 - -",
-                    "@PG\tID:samtools.2.extra_header\tPN:samtools\tPP:samtools.1\tVN:1.22.1\tCL:samtools sort -u -T mMelMel3_T4.sort --threads 4 -",
-                    "@PG\tID:samtools.3.extra_header\tPN:samtools\tPP:samtools.2\tVN:1.22.1\tCL:samtools markdup -T mMelMel3_T4.markdup -f mMelMel3_T4.metrics --threads 4 - mMelMel3_T4.cram",
-                    "@PG\tID:samtools.4.extra_header\tPN:samtools\tPP:samtools.3\tVN:1.23.1\tCL:samtools view -H m64094_200911_174739.ccs.bc1022_BAK8B_OA--bc1022_BAK8B_OA.subset.cram",
+                    "@PG\tID:samtools.1.extra_header\tPN:samtools\tPP:samtools.extra_header\tVN:1.22.1\tCL:samtools fixmate -m -u --threads 4 - -",
+                    "@PG\tID:samtools.2.extra_header\tPN:samtools\tPP:samtools.1.extra_header\tVN:1.22.1\tCL:samtools sort -u -T mMelMel3_T4.sort --threads 4 -",
+                    "@PG\tID:samtools.3.extra_header\tPN:samtools\tPP:samtools.2.extra_header\tVN:1.22.1\tCL:samtools markdup -T mMelMel3_T4.markdup -f mMelMel3_T4.metrics --threads 4 - mMelMel3_T4.cram",
+                    "@PG\tID:samtools.4.extra_header\tPN:samtools\tPP:samtools.3.extra_header\tVN:1.23.1\tCL:samtools view -H m64094_200911_174739.ccs.bc1022_BAK8B_OA--bc1022_BAK8B_OA.subset.cram",
                     "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t4 -ax map-hifi --cs=short -y -R @RG\\tID:m64094_200911_174739\\tPL:PACBIO\\tSM:SAMEA7524440 -I1G -a GCA_922984935.2.subset.unmasked.mmi -",
                     "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.23.1\tCL:samtools sort -@ 3 -o m64094_200911_174739.ccs.bc1022_BAK8B_OA--bc1022_BAK8B_OA.subset.fastq.gz.0.SAMEA7524440.ERR6939249.bam -T m64094_200911_174739.ccs.bc1022_BAK8B_OA--bc1022_BAK8B_OA.subset.fastq.gz.0.SAMEA7524440.ERR6939249_sort_tmp --write-index -l1 -",
                     "@PG\tID:samtools.1\tPN:samtools\tPP:samtools\tVN:1.23.1\tCL:samtools merge --threads 3 -c -p --reference GCA_922984935.2.subset.unmasked.fa SAMEA7524440.ERR6939249.merge.bam 1/m64094_200911_174739.ccs.bc1022_BAK8B_OA--bc1022_BAK8B_OA.subset.fastq.gz.0.SAMEA7524440.ERR6939249.bam",
                     "@PG\tID:crumble\tPN:crumble\tPP:samtools.1\tVN:0.9.1\tCL:crumble -y pbccs -O bam SAMEA7524440.ERR6939249.merge.bam SAMEA7524440.ERR6939249.merge.crumble.bam",
-                    "@PG\tID:samtools.2\tPN:samtools\tPP:samtools.1.extra_header\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.bam",
-                    "@PG\tID:samtools.3\tPN:samtools\tPP:samtools.2.extra_header\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.bam",
-                    "@PG\tID:samtools.4\tPN:samtools\tPP:crumble\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.bam",
-                    "@PG\tID:samtools.5\tPN:samtools\tPP:samtools.3.extra_header\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.bam",
-                    "@PG\tID:samtools.6\tPN:samtools\tPP:samtools.4.extra_header\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.bam",
-                    "@PG\tID:samtools.7\tPN:samtools\tPP:samtools.4\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.bam"
+                    "@PG\tID:samtools.2\tPN:samtools\tPP:samtools.4.extra_header\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.bam",
+                    "@PG\tID:samtools.3\tPN:samtools\tPP:crumble\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.bam",
+                    "@PG\tID:samtools.4\tPN:samtools\tPP:samtools.2\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.bam",
+                    "@PG\tID:samtools.5\tPN:samtools\tPP:samtools.3\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.bam"
                 ],
                 "GCA_922984935.2.subset.pacbio.SAMEA7524440.merged_1.minimap2.bam": [
                     "@HD\tVN:1.6\tSO:coordinate",
@@ -261,6 +259,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.4"
         },
-        "timestamp": "2026-05-29T01:47:41.430447254"
+        "timestamp": "2026-05-29T03:12:18.823237748"
     }
 }
\ No newline at end of file

From bf2636393b4169a91b68d32b47290d67071a35cb Mon Sep 17 00:00:00 2001
From: sainsachiko <hthhanh.work@gmail.com>
Date: Fri, 29 May 2026 03:27:14 +0100
Subject: [PATCH 09/20] Fix grammar

---
 docs/usage.md | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/docs/usage.md b/docs/usage.md
index e11bff39..4c9294da 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -40,15 +40,15 @@ specimen2,run4,pacbio,pacbio1.bam,uli,,headers/pacbio_rg.sam
 specimen3,run5,pacbio,pacbio2.bam,,,
 ```
 
-| Column         | Description                                                                                                                                                                                                                                                                            |
-| -------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| `specimen`     | Identifier of the specimen. Usually a BioSpecimen accession, i,e. `SAMEA7521529`.                                                                                                                                                                                                      |
-| `run`          | Identifier of the sequencing run. Usually the accession number of the data in INSDC. For example,`ERR9248445` (hic), `ERR9284044` (pacbio).                                                                                                                                            |
-| `datatype`     | Type of sequencing data. Must be one of `hic`, `illumina`, `pacbio`, `pacbio_clr`, or `ont`.                                                                                                                                                                                           |
-| `datafile`     | Full path to read data file. Must be `bam`, `cram`, `fastq.gz` or `fq.gz` for `illumina` and `hic`. Must be `bam`, `fastq.gz` or `fq.gz` for `pacbio`, `pacbio_clr`, and `ont`. Note that FASTQ inputs should be interleaved if paired-end.                                            |
-| `library`      | (Optional) The library value is a unique identifier which is assigned to read group (`@RG`) ID. If the library name is not specified, the pipeline will auto-create library name using the data filename provided in the samplesheet.                                                  |
-| `barcode`      | (Optional) Barcode identifier used to trim barcode adapter for PacBio reads. If empty, barcode-specific adapter sequences will not be trimmed.                                                                                                                                         |
-| `extra_header` | (Optional) Path to a SAM file containing additional SAM header lines including `@RG`, `@PG`. These information will be injected into output BAM/CRAM headers. `@RG` lines are overwritten, while `@PG` lines are added to the existing headers (auto add `.extra_header` to `@PG ID`). |
+| Column         | Description                                                                                                                                                                                                                                                                           |
+| -------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| `specimen`     | Identifier of the specimen. Usually a BioSpecimen accession, i,e. `SAMEA7521529`.                                                                                                                                                                                                     |
+| `run`          | Identifier of the sequencing run. Usually the accession number of the data in INSDC. For example,`ERR9248445` (hic), `ERR9284044` (pacbio).                                                                                                                                           |
+| `datatype`     | Type of sequencing data. Must be one of `hic`, `illumina`, `pacbio`, `pacbio_clr`, or `ont`.                                                                                                                                                                                          |
+| `datafile`     | Full path to read data file. Must be `bam`, `cram`, `fastq.gz` or `fq.gz` for `illumina` and `hic`. Must be `bam`, `fastq.gz` or `fq.gz` for `pacbio`, `pacbio_clr`, and `ont`. Note that FASTQ inputs should be interleaved if paired-end.                                           |
+| `library`      | (Optional) The library value is a unique identifier which is assigned to read group (`@RG`) ID. If the library name is not specified, the pipeline will auto-create library name using the data filename provided in the samplesheet.                                                 |
+| `barcode`      | (Optional) Barcode identifier used to trim barcode adapter for PacBio reads. If empty, barcode-specific adapter sequences will not be trimmed.                                                                                                                                        |
+| `extra_header` | (Optional) Path to a SAM file containing additional SAM header lines including `@RG`, `@PG`. This information will be injected into output BAM/CRAM headers. `@RG` lines are overwritten, while `@PG` lines are added to the existing headers (auto add `.extra_header` to `@PG ID`). |
 
 An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline.
 

From 61a9d06295b1e9c1a1858e1ffae127d5c2324741 Mon Sep 17 00:00:00 2001
From: sainsachiko <hthhanh.work@gmail.com>
Date: Fri, 29 May 2026 04:11:14 +0100
Subject: [PATCH 10/20] For test no header, keep filename only

---
 tests/uli.nf.test         |  2 +-
 tests/uli.nf.test.snap    | 18 +++++++++---------
 tests/uli_no_lima.nf.test |  2 +-
 3 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/tests/uli.nf.test b/tests/uli.nf.test
index befcb382..a21e05a1 100644
--- a/tests/uli.nf.test
+++ b/tests/uli.nf.test
@@ -34,7 +34,7 @@ nextflow_pipeline {
                 lines
                     .collect { line ->
                         line.toString()
-                            .replaceAll(/\bUR:\/(?:([^\/\s]+)\/([^\/\s]+)\/([^\/\s]+))\/\S+/, 'UR:/$1/$2/$3/<ABS_PATH>')
+                            .replaceAll(/\bUR:\/(?:[^\/\s]+\/)*([^\/\s]+)/, 'UR:$1')
                             .replaceAll(/(^|\s)\/(?:[^\s\/]+\/)+[^\s\/]+/, '$1<ABS_PATH>')
                     }
             }
diff --git a/tests/uli.nf.test.snap b/tests/uli.nf.test.snap
index cbc2ae1b..31372cd3 100644
--- a/tests/uli.nf.test.snap
+++ b/tests/uli.nf.test.snap
@@ -175,10 +175,10 @@
             {
                 "GCA_964034985.1.subset.pacbio.SAMEA114784749.ERR14209104.minimap2.cram": [
                     "@HD\tVN:1.6\tSO:coordinate",
-                    "@SQ\tSN:CAXIUN010000020.1\tLN:15094\tM5:eb4b4e09fa2962e012fc983eeb6b65dc\tUR:/lustre/scratch124/tol/<ABS_PATH>",
-                    "@SQ\tSN:CAXIUN010000038.1\tLN:1000\tM5:3fe8a9b5a85c60b19e74e88ca5ca434e\tUR:/lustre/scratch124/tol/<ABS_PATH>",
-                    "@SQ\tSN:CAXIUN010000104.1\tLN:10110\tM5:10013ae295fb0e1a002ab812d6c2e77e\tUR:/lustre/scratch124/tol/<ABS_PATH>",
-                    "@SQ\tSN:CAXIUN010000129.1\tLN:29940\tM5:9579779c87681c88e68a924f572f5599\tUR:/lustre/scratch124/tol/<ABS_PATH>",
+                    "@SQ\tSN:CAXIUN010000020.1\tLN:15094\tM5:eb4b4e09fa2962e012fc983eeb6b65dc\tUR:GCA_964034985.1.subset.unmasked.fa",
+                    "@SQ\tSN:CAXIUN010000038.1\tLN:1000\tM5:3fe8a9b5a85c60b19e74e88ca5ca434e\tUR:GCA_964034985.1.subset.unmasked.fa",
+                    "@SQ\tSN:CAXIUN010000104.1\tLN:10110\tM5:10013ae295fb0e1a002ab812d6c2e77e\tUR:GCA_964034985.1.subset.unmasked.fa",
+                    "@SQ\tSN:CAXIUN010000129.1\tLN:29940\tM5:9579779c87681c88e68a924f572f5599\tUR:GCA_964034985.1.subset.unmasked.fa",
                     "@RG\tID:0de7f0a4/27--27\tPL:PACBIO\tDS:READTYPE=CCS;Ipd:CodecV1=ip;PulseWidth:CodecV1=pw;BINDINGKIT=102-739-100;SEQUENCINGKIT=102-118-800;BASECALLERVERSION=5.0;SMRTCELLKIT=102-202-200;SMRTCELLID=EA138735;RUNID=r84093_20241115_102726;ICSVERSION=13.0.0.212033;MOVIELENGTH=1440.0;FRAMERATEHZ=100.000000;BarcodeFile=metadata/m84093_241116_151316_s2.barcodes.fasta;BarcodeHash=86d73e586a6d3ede0295785b51105eea;BarcodeCount=96;BarcodeMode=Symmetric;BarcodeQuality=Score\tLB:TRAC-2-8053\tPU:m84093_241116_151316_s2\tSM:TOL_ASG14652249\tPM:REVIO\tBC:ACTGCAGCACGAGTAT\tCM:R/P1-C1/5.0-25M",
                     "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t4 -ax map-hifi --cs=short -y -R @RG\\tID:0de7f0a4/27--27\\tPL:PACBIO\\tDS:READTYPE=CCS;Ipd:CodecV1=ip;PulseWidth:CodecV1=pw;BINDINGKIT=102-739-100;SEQUENCINGKIT=102-118-800;BASECALLERVERSION=5.0;SMRTCELLKIT=102-202-200;SMRTCELLID=EA138735;RUNID=r84093_20241115_102726;ICSVERSION=13.0.0.212033;MOVIELENGTH=1440.0;FRAMERATEHZ=100.000000;BarcodeFile=metadata/m84093_241116_151316_s2.barcodes.fasta;BarcodeHash=86d73e586a6d3ede0295785b51105eea;BarcodeCount=96;BarcodeMode=Symmetric;BarcodeQuality=Score\\tLB:TRAC-2-8053\\tPU:m84093_241116_151316_s2\\tSM:TOL_ASG14652249\\tPM:REVIO\\tBC:ACTGCAGCACGAGTAT\\tCM:R/P1-C1/5.0-25M -I1G -a GCA_964034985.1.subset.unmasked.mmi -",
                     "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.23.1\tCL:samtools sort -@ 3 -o pacbio.SAMEA114784749.ERR14209104.hifitrimmer.fastq.gz.0.SAMEA114784749.ERR14209104.bam -T pacbio.SAMEA114784749.ERR14209104.hifitrimmer.fastq.gz.0.SAMEA114784749.ERR14209104_sort_tmp --write-index -l1 -",
@@ -188,10 +188,10 @@
                 ],
                 "GCA_964034985.1.subset.pacbio.SAMEA114784749.ERR14209104_test.minimap2.cram": [
                     "@HD\tVN:1.6\tSO:coordinate",
-                    "@SQ\tSN:CAXIUN010000020.1\tLN:15094\tM5:eb4b4e09fa2962e012fc983eeb6b65dc\tUR:/lustre/scratch124/tol/<ABS_PATH>",
-                    "@SQ\tSN:CAXIUN010000038.1\tLN:1000\tM5:3fe8a9b5a85c60b19e74e88ca5ca434e\tUR:/lustre/scratch124/tol/<ABS_PATH>",
-                    "@SQ\tSN:CAXIUN010000104.1\tLN:10110\tM5:10013ae295fb0e1a002ab812d6c2e77e\tUR:/lustre/scratch124/tol/<ABS_PATH>",
-                    "@SQ\tSN:CAXIUN010000129.1\tLN:29940\tM5:9579779c87681c88e68a924f572f5599\tUR:/lustre/scratch124/tol/<ABS_PATH>",
+                    "@SQ\tSN:CAXIUN010000020.1\tLN:15094\tM5:eb4b4e09fa2962e012fc983eeb6b65dc\tUR:GCA_964034985.1.subset.unmasked.fa",
+                    "@SQ\tSN:CAXIUN010000038.1\tLN:1000\tM5:3fe8a9b5a85c60b19e74e88ca5ca434e\tUR:GCA_964034985.1.subset.unmasked.fa",
+                    "@SQ\tSN:CAXIUN010000104.1\tLN:10110\tM5:10013ae295fb0e1a002ab812d6c2e77e\tUR:GCA_964034985.1.subset.unmasked.fa",
+                    "@SQ\tSN:CAXIUN010000129.1\tLN:29940\tM5:9579779c87681c88e68a924f572f5599\tUR:GCA_964034985.1.subset.unmasked.fa",
                     "@RG\tID:0de7f0a4/27--27\tPL:PACBIO\tDS:READTYPE=CCS;Ipd:CodecV1=ip;PulseWidth:CodecV1=pw;BINDINGKIT=102-739-100;SEQUENCINGKIT=102-118-800;BASECALLERVERSION=5.0;SMRTCELLKIT=102-202-200;SMRTCELLID=EA138735;RUNID=r84093_20241115_102726;ICSVERSION=13.0.0.212033;MOVIELENGTH=1440.0;FRAMERATEHZ=100.000000;BarcodeFile=metadata/m84093_241116_151316_s2.barcodes.fasta;BarcodeHash=86d73e586a6d3ede0295785b51105eea;BarcodeCount=96;BarcodeMode=Symmetric;BarcodeQuality=Score\tLB:TRAC-2-8053\tPU:m84093_241116_151316_s2\tSM:TOL_ASG14652249\tPM:REVIO\tBC:ACTGCAGCACGAGTAT\tCM:R/P1-C1/5.0-25M",
                     "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t4 -ax map-hifi --cs=short -y -R @RG\\tID:0de7f0a4/27--27\\tPL:PACBIO\\tDS:READTYPE=CCS;Ipd:CodecV1=ip;PulseWidth:CodecV1=pw;BINDINGKIT=102-739-100;SEQUENCINGKIT=102-118-800;BASECALLERVERSION=5.0;SMRTCELLKIT=102-202-200;SMRTCELLID=EA138735;RUNID=r84093_20241115_102726;ICSVERSION=13.0.0.212033;MOVIELENGTH=1440.0;FRAMERATEHZ=100.000000;BarcodeFile=metadata/m84093_241116_151316_s2.barcodes.fasta;BarcodeHash=86d73e586a6d3ede0295785b51105eea;BarcodeCount=96;BarcodeMode=Symmetric;BarcodeQuality=Score\\tLB:TRAC-2-8053\\tPU:m84093_241116_151316_s2\\tSM:TOL_ASG14652249\\tPM:REVIO\\tBC:ACTGCAGCACGAGTAT\\tCM:R/P1-C1/5.0-25M -I1G -a GCA_964034985.1.subset.unmasked.mmi -",
                     "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.23.1\tCL:samtools sort -@ 3 -o pacbio.SAMEA114784749.ERR14209104_test.hifitrimmer.fastq.gz.0.SAMEA114784749.ERR14209104_test.bam -T pacbio.SAMEA114784749.ERR14209104_test.hifitrimmer.fastq.gz.0.SAMEA114784749.ERR14209104_test_sort_tmp --write-index -l1 -",
@@ -209,6 +209,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.4"
         },
-        "timestamp": "2026-05-29T00:46:30.255398793"
+        "timestamp": "2026-05-29T03:53:26.611534435"
     }
 }
\ No newline at end of file
diff --git a/tests/uli_no_lima.nf.test b/tests/uli_no_lima.nf.test
index 7db645a8..272164c2 100644
--- a/tests/uli_no_lima.nf.test
+++ b/tests/uli_no_lima.nf.test
@@ -36,7 +36,7 @@ nextflow_pipeline {
                 lines
                     .collect { line ->
                         line.toString()
-                            .replaceAll(/\bUR:\/(?:([^\/\s]+)\/([^\/\s]+)\/([^\/\s]+))\/\S+/, 'UR:/$1/$2/$3/<ABS_PATH>')
+                            .replaceAll(/\bUR:\/(?:[^\/\s]+\/)*([^\/\s]+)/, 'UR:$1')
                             .replaceAll(/(^|\s)\/(?:[^\s\/]+\/)+[^\s\/]+/, '$1<ABS_PATH>')
                     }
             }

From e77498b1bcfd475044704e0f547105e747321acc Mon Sep 17 00:00:00 2001
From: sainsachiko <hthhanh.work@gmail.com>
Date: Fri, 29 May 2026 04:12:53 +0100
Subject: [PATCH 11/20] Removed tDT in RG for snapshot of test minimap2 as
 short aligner

---
 tests/short_aligner_minimap2.nf.test      | 1 +
 tests/short_aligner_minimap2.nf.test.snap | 6 +++---
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/tests/short_aligner_minimap2.nf.test b/tests/short_aligner_minimap2.nf.test
index e129528c..fecd4327 100644
--- a/tests/short_aligner_minimap2.nf.test
+++ b/tests/short_aligner_minimap2.nf.test
@@ -37,6 +37,7 @@ nextflow_pipeline {
                     .collect { line ->
                             line.toString()
                                 .replaceAll(/\bUR:\/((?:[^\/\s]+\/){2})\S+/, 'UR:/$1<ABS_PATH>')
+                                .replaceAll(/\tDT:[^\t\n]+/, '')
                     }
             }
 
diff --git a/tests/short_aligner_minimap2.nf.test.snap b/tests/short_aligner_minimap2.nf.test.snap
index 8926f46d..9d955622 100644
--- a/tests/short_aligner_minimap2.nf.test.snap
+++ b/tests/short_aligner_minimap2.nf.test.snap
@@ -259,7 +259,7 @@
                 "GCA_922984935.2.subset.illumina.SAMEA7524438.ERR6688599.minimap2.bam": [
                     "@HD\tVN:1.6\tSO:coordinate",
                     "@SQ\tSN:OV277441.1\tLN:7999920\tM5:0457acf8690429f1c98ee545cb8573b8\tUR:/nfs/treeoflife-01/<ABS_PATH>\tAS:GCA_922984935.2\tAN:SUPER_1\tSP:Meles meles",
-                    "@RG\tID:31231_3#1\tDT:2019-10-03T01:00:00+0100\tPU:191003_HX4_31231_A_H3353CCX2_3#1\tLB:23687379\tPG:SCS\tSM:SAMEA5962962\tCN:SC\tPL:ILLUMINA\tDS:ERP114452: Sequencing and assembly of vertebrate genomes from British species for the Darwin Tree of Life Project in collaboration with the Vertebrate Genomes Project. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",
+                    "@RG\tID:31231_3#1\tPU:191003_HX4_31231_A_H3353CCX2_3#1\tLB:23687379\tPG:SCS\tSM:SAMEA5962962\tCN:SC\tPL:ILLUMINA\tDS:ERP114452: Sequencing and assembly of vertebrate genomes from British species for the Darwin Tree of Life Project in collaboration with the Vertebrate Genomes Project. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",
                     "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t4 -ax sr --cs=short -I1.0G -y -R @RG\\tID:31231_3#1\\tDT:2019-10-03T00:00:00+0000\\tPU:191003_HX4_31231_A_H3353CCX2_3#1\\tLB:23687379\\tPG:SCS\\tSM:SAMEA5962962\\tCN:SC\\tPL:ILLUMINA\\tDS:ERP114452: Sequencing and assembly of vertebrate genomes from British species for the Darwin Tree of Life Project in collaboration with the Vertebrate Genomes Project. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ GCA_922984935.2.subset.unmasked.mmi -",
                     "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.22.1\tCL:samtools fixmate -mpu - -",
                     "@PG\tID:samtools.1\tPN:samtools\tPP:samtools\tVN:1.22.1\tCL:samtools view -h",
@@ -321,7 +321,7 @@
                 "GCA_922984935.2.subset.illumina.SAMEA7524438.ERR6688599.minimap2.cram": [
                     "@HD\tVN:1.6\tSO:coordinate",
                     "@SQ\tSN:OV277441.1\tLN:7999920\tM5:0457acf8690429f1c98ee545cb8573b8\tUR:/nfs/treeoflife-01/<ABS_PATH>\tAS:GCA_922984935.2\tAN:SUPER_1\tSP:Meles meles",
-                    "@RG\tID:31231_3#1\tDT:2019-10-03T01:00:00+0100\tPU:191003_HX4_31231_A_H3353CCX2_3#1\tLB:23687379\tPG:SCS\tSM:SAMEA5962962\tCN:SC\tPL:ILLUMINA\tDS:ERP114452: Sequencing and assembly of vertebrate genomes from British species for the Darwin Tree of Life Project in collaboration with the Vertebrate Genomes Project. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",
+                    "@RG\tID:31231_3#1\tPU:191003_HX4_31231_A_H3353CCX2_3#1\tLB:23687379\tPG:SCS\tSM:SAMEA5962962\tCN:SC\tPL:ILLUMINA\tDS:ERP114452: Sequencing and assembly of vertebrate genomes from British species for the Darwin Tree of Life Project in collaboration with the Vertebrate Genomes Project. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",
                     "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t4 -ax sr --cs=short -I1.0G -y -R @RG\\tID:31231_3#1\\tDT:2019-10-03T00:00:00+0000\\tPU:191003_HX4_31231_A_H3353CCX2_3#1\\tLB:23687379\\tPG:SCS\\tSM:SAMEA5962962\\tCN:SC\\tPL:ILLUMINA\\tDS:ERP114452: Sequencing and assembly of vertebrate genomes from British species for the Darwin Tree of Life Project in collaboration with the Vertebrate Genomes Project. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ GCA_922984935.2.subset.unmasked.mmi -",
                     "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.22.1\tCL:samtools fixmate -mpu - -",
                     "@PG\tID:samtools.1\tPN:samtools\tPP:samtools\tVN:1.22.1\tCL:samtools view -h",
@@ -355,6 +355,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.4"
         },
-        "timestamp": "2026-05-29T03:07:26.580580159"
+        "timestamp": "2026-05-29T04:12:24.650580553"
     }
 }
\ No newline at end of file

From a4f205b3876dcb54a642fa364ed87f307bd1d410 Mon Sep 17 00:00:00 2001
From: sainsachiko <hthhanh.work@gmail.com>
Date: Wed, 3 Jun 2026 15:37:44 +0100
Subject: [PATCH 12/20] Fix UTC timezone for nf-test

---
 nf-test.config                       | 4 ++++
 tests/short_aligner_minimap2.nf.test | 1 -
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/nf-test.config b/nf-test.config
index 0b2e3c59..27fd64a7 100644
--- a/nf-test.config
+++ b/nf-test.config
@@ -1,3 +1,7 @@
+// Force UTC so DT fields in BAM/CRAM headers don't shift across DST
+System.setProperty('user.timezone', 'UTC')
+TimeZone.setDefault(TimeZone.getTimeZone('UTC'))
+
 config {
     // location for all nf-test tests
     testsDir "."
diff --git a/tests/short_aligner_minimap2.nf.test b/tests/short_aligner_minimap2.nf.test
index fecd4327..e129528c 100644
--- a/tests/short_aligner_minimap2.nf.test
+++ b/tests/short_aligner_minimap2.nf.test
@@ -37,7 +37,6 @@ nextflow_pipeline {
                     .collect { line ->
                             line.toString()
                                 .replaceAll(/\bUR:\/((?:[^\/\s]+\/){2})\S+/, 'UR:/$1<ABS_PATH>')
-                                .replaceAll(/\tDT:[^\t\n]+/, '')
                     }
             }
 

From a70a591deb871c3b3426bbf7d9a73bd1768306c0 Mon Sep 17 00:00:00 2001
From: sainsachiko <hthhanh.work@gmail.com>
Date: Wed, 3 Jun 2026 16:06:32 +0100
Subject: [PATCH 13/20] Test snapshot: Replace abs path with file name

---
 tests/default.nf.test                | 2 +-
 tests/short_aligner_minimap2.nf.test | 2 +-
 tests/uli.nf.test                    | 1 -
 tests/uli_no_lima.nf.test            | 1 -
 tests/untrim.nf.test                 | 3 +--
 5 files changed, 3 insertions(+), 6 deletions(-)

diff --git a/tests/default.nf.test b/tests/default.nf.test
index e827d4a4..5f591b09 100644
--- a/tests/default.nf.test
+++ b/tests/default.nf.test
@@ -34,7 +34,7 @@ nextflow_pipeline {
                 lines
                     .collect { line ->
                         line.toString()
-                            .replaceAll(/\bUR:\/((?:[^\/\s]+\/){2})\S+/, 'UR:/$1<ABS_PATH>')
+                            .replaceAll(/\bUR:\/(?:[^\/\s]+\/)*([^\/\s]+)/, 'UR:$1')
                     }
             }
 
diff --git a/tests/short_aligner_minimap2.nf.test b/tests/short_aligner_minimap2.nf.test
index e129528c..3d4914c2 100644
--- a/tests/short_aligner_minimap2.nf.test
+++ b/tests/short_aligner_minimap2.nf.test
@@ -36,7 +36,7 @@ nextflow_pipeline {
                 lines
                     .collect { line ->
                             line.toString()
-                                .replaceAll(/\bUR:\/((?:[^\/\s]+\/){2})\S+/, 'UR:/$1<ABS_PATH>')
+                            .replaceAll(/\bUR:\/(?:[^\/\s]+\/)*([^\/\s]+)/, 'UR:$1')
                     }
             }
 
diff --git a/tests/uli.nf.test b/tests/uli.nf.test
index a21e05a1..7656457f 100644
--- a/tests/uli.nf.test
+++ b/tests/uli.nf.test
@@ -35,7 +35,6 @@ nextflow_pipeline {
                     .collect { line ->
                         line.toString()
                             .replaceAll(/\bUR:\/(?:[^\/\s]+\/)*([^\/\s]+)/, 'UR:$1')
-                            .replaceAll(/(^|\s)\/(?:[^\s\/]+\/)+[^\s\/]+/, '$1<ABS_PATH>')
                     }
             }
 
diff --git a/tests/uli_no_lima.nf.test b/tests/uli_no_lima.nf.test
index 272164c2..99c780b6 100644
--- a/tests/uli_no_lima.nf.test
+++ b/tests/uli_no_lima.nf.test
@@ -37,7 +37,6 @@ nextflow_pipeline {
                     .collect { line ->
                         line.toString()
                             .replaceAll(/\bUR:\/(?:[^\/\s]+\/)*([^\/\s]+)/, 'UR:$1')
-                            .replaceAll(/(^|\s)\/(?:[^\s\/]+\/)+[^\s\/]+/, '$1<ABS_PATH>')
                     }
             }
 
diff --git a/tests/untrim.nf.test b/tests/untrim.nf.test
index d1736f4a..925013bf 100644
--- a/tests/untrim.nf.test
+++ b/tests/untrim.nf.test
@@ -38,8 +38,7 @@ nextflow_pipeline {
                 lines
                     .collect { line ->
                         line.toString()
-                            .replaceAll(/\bUR:\/(?:([^\/\s]+)\/([^\/\s]+)\/([^\/\s]+))\/\S+/, 'UR:/$1/$2/$3/<ABS_PATH>')
-                            .replaceAll(/(^|\s)\/(?:[^\s\/]+\/)+[^\s\/]+/, '$1<ABS_PATH>')
+                            .replaceAll(/\bUR:\/(?:[^\/\s]+\/)*([^\/\s]+)/, 'UR:$1')
                     }
             }
 

From e9c043d84fdfa4c982dc6e13817c98cbd2520a53 Mon Sep 17 00:00:00 2001
From: sainsachiko <hthhanh.work@gmail.com>
Date: Wed, 3 Jun 2026 16:07:36 +0100
Subject: [PATCH 14/20] Fix logic of handling RG

---
 subworkflows/local/prepare_read_groups.nf | 87 +++++++++++++----------
 1 file changed, 49 insertions(+), 38 deletions(-)

diff --git a/subworkflows/local/prepare_read_groups.nf b/subworkflows/local/prepare_read_groups.nf
index 8f87f196..d97750ec 100644
--- a/subworkflows/local/prepare_read_groups.nf
+++ b/subworkflows/local/prepare_read_groups.nf
@@ -2,7 +2,8 @@
 // Prepare read-group metadata from optional extra_header and BAM input headers
 //
 
-include { SAMTOOLS_SPLITHEADER } from '../../modules/nf-core/samtools/splitheader/main'
+include { SAMTOOLS_SPLITHEADER as SAMTOOLS_SPLITHEADER_EXTRA } from '../../modules/nf-core/samtools/splitheader/main'
+include { SAMTOOLS_SPLITHEADER as SAMTOOLS_SPLITHEADER_BAM   } from '../../modules/nf-core/samtools/splitheader/main'
 
 workflow PREPARE_READ_GROUPS {
     take:
@@ -15,49 +16,59 @@ workflow PREPARE_READ_GROUPS {
     def rg_flag = rg_mode == 'long' ? '-R' : '-r'
 
     // Pre-populate read_group for all inputs; downstream steps may override it from extracted @RG lines
-    ch_reads_prefixed = reads.map { meta, read_file -> [meta + [read_group: "${rg_lead} ${rg_flag} $meta.read_group", replace_rg: true], read_file] }
+    ch_reads_prefixed = reads.map { meta, read_file ->
+        [meta + [read_group: "${rg_lead} ${rg_flag} $meta.read_group", replace_rg: true, read_file: read_file], read_file]
+    }
 
-    ch_reads_extra_header = ch_reads_prefixed
-        .branch { meta, read_file ->
-            // Inputs with explicit extra_header metadata should be parsed directly
-            has_extra_header: meta.extra_header != []
-                return [meta + [read_file: read_file], meta.extra_header]
-            // For BAM/CRAM without extra_header metadata, extract header from the alignment file.
-            no_extra_header_bam_cram: meta.extra_header == [] && read_file.name ==~ /.*\.(bam|cram)$/
-            // FASTQ and remaining inputs keep the pre-populated read_group.
-            no_extra_header_fastq: true
-        }
+    ch_branched = ch_reads_prefixed.branch { meta, read_file ->
+        // An input may match both extra and bam_cram extraction: extra_header is parsed here; BAM/CRAM is also parsed below as an independent fallback source
+        has_extra: meta.extra_header != []
+            return [meta, meta.extra_header]
+        fastq:     !(read_file.name ==~ /.*\.(bam|cram)$/)
+        other:     true
+    }
+    ch_bam_cram = ch_reads_prefixed.filter { _meta, read_file -> read_file.name ==~ /.*\.(bam|cram)$/ }
+
+    // Extract @RG/@PG from extra_header files and (independently) from BAM/CRAM alignment files
+    SAMTOOLS_SPLITHEADER_EXTRA(ch_branched.has_extra)
+    SAMTOOLS_SPLITHEADER_BAM(ch_bam_cram)
 
-    // Extract @RG/@PG from provided extra_header files and BAM/CRAM headers
-    SAMTOOLS_SPLITHEADER(ch_reads_extra_header.has_extra_header.mix(ch_reads_extra_header.no_extra_header_bam_cram))
+    // Tag each result with its source so the resolver can pick precedence: extra_header > bam > precomputed
+    ch_extra = SAMTOOLS_SPLITHEADER_EXTRA.out.readgroup.join(SAMTOOLS_SPLITHEADER_EXTRA.out.programs).map { it + ['extra'] }
+    ch_bam   = SAMTOOLS_SPLITHEADER_BAM.out.readgroup.join(SAMTOOLS_SPLITHEADER_BAM.out.programs).map { it + ['bam'] }
 
-    ch_reads_with_rg = SAMTOOLS_SPLITHEADER.out.readgroup
-        .join(SAMTOOLS_SPLITHEADER.out.programs)
-        .join(ch_reads_extra_header.has_extra_header.mix(ch_reads_extra_header.no_extra_header_bam_cram), by: 0)
-        .map { meta, rg_file, program_file, read_files ->
-            def rglines = file(rg_file).readLines()
-            // Prefer extracted @RG lines; fallback to the existing read_group only when extraction is empty
-            def rg_args = rglines ? [
-                rg_lead,
-                rglines.collect { line ->
-                    // Add SM when not present to avoid errors from downstream tools (e.g. variant callers)
-                    def l = line.contains('SM:') ? line
-                            : meta.sample ? "${line}\tSM:${meta.sample}"
-                            : "${line}\tSM:${meta.id}"
-                    "${rg_flag} '${l.replaceAll("\t", "\\\\t")}'"
-                }.join(' ')
-            ].findAll { value -> value }.join(' ')
+    // Group all extracted headers per meta; inputs may yield 0, 1 (extra or bam only), or 2 (both) entries
+    ch_resolved = ch_extra.mix(ch_bam)
+        .map { meta, rg, pg, src -> [meta.id, meta, rg, pg, src] }
+        .groupTuple()
+        .map { _id, metas, rgs, pgs, srcs ->
+            def meta = metas[0]
+            def bySrc = [srcs, rgs, pgs].transpose().collectEntries { src, rg, pg -> [(src): [rg: rg, pg: pg]] }
+            // RG: prefer extra_header lines; fall back to BAM @RG; finally fall back to precomputed meta.read_group
+            def picked_rg = ['extra', 'bam'].findResult { src ->
+                def entry = bySrc[src]
+                if (!entry) return null
+                def lines = file(entry.rg).readLines()
+                lines ? [src: src, rglines: lines] : null
+            }
+            // PG: inject @PG downstream only when extra_header supplies them; otherwise preserve whatever the BAM/CRAM already has
+            def extra_has_pg = bySrc.extra && !file(bySrc.extra.pg).readLines().isEmpty()
+
+            def from_bam = picked_rg?.src == 'bam'
+            def rg_args = picked_rg ? [rg_lead, picked_rg.rglines.collect { line ->
+                // Add SM when not present to avoid errors from downstream tools (e.g. variant callers)
+                def l = line.contains('SM:') ? line : "${line}\tSM:${meta.sample ?: meta.id}"
+                "${rg_flag} '${l.replaceAll('\t', '\\\\t')}'"
+            }.join(' ')].findAll().join(' ')
             : (meta.read_group ?: '')
 
-            def output_read_files = meta.read_file ?: read_files
-            // If RG came from an existing BAM/CRAM header, and no extra RG provided to overwrite, preserve it and avoid replacing downstream
-            // If PG came from an existing BAM/CRAM header, and no extra PG provided to overwrite, preserve it and avoid replacing downstream
-            def replace_rg = !meta.extra_header && rglines ? false : true
-            def add_pg = !meta.extra_header && program_file ? false : true
-            def new_meta = meta.subMap(meta.keySet() - ['read_file']) + [read_group: rg_args, replace_rg: replace_rg, add_pg: add_pg]
-            [new_meta, output_read_files]
+            // Don't replace RG when it already comes from the BAM/CRAM header itself
+            def replace_rg = !(from_bam && picked_rg)
+            def new_meta = meta.subMap(meta.keySet() - ['read_file']) + [read_group: rg_args, replace_rg: replace_rg, add_pg: extra_has_pg]
+            [new_meta, meta.read_file]
         }
-        .mix(ch_reads_extra_header.no_extra_header_fastq)
+
+    ch_reads_with_rg = ch_resolved.mix(ch_branched.fastq.map { meta, rf -> [meta.subMap(meta.keySet() - ['read_file']), rf] })
 
     emit:
     reads = ch_reads_with_rg               // channel: [ val(meta), /path/to/read_file ]

From ebf6fd1a3434773dfdfecc9fc5233e60935fa1eb Mon Sep 17 00:00:00 2001
From: sainsachiko <hthhanh.work@gmail.com>
Date: Wed, 3 Jun 2026 17:08:05 +0100
Subject: [PATCH 15/20] Update Snapshots

---
 tests/default.nf.test.snap                | 55 ++++++++++++-----------
 tests/short_aligner_minimap2.nf.test.snap | 40 ++++++++++-------
 tests/uli.nf.test.snap                    |  4 +-
 tests/uli_no_lima.nf.test.snap            |  4 +-
 tests/untrim.nf.test.snap                 | 34 +++++++-------
 5 files changed, 75 insertions(+), 62 deletions(-)

diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap
index 13ed1309..da6fbc45 100644
--- a/tests/default.nf.test.snap
+++ b/tests/default.nf.test.snap
@@ -1,7 +1,7 @@
 {
     "-profile test": {
         "content": [
-            182,
+            183,
             {
                 "BGZIP_BEDGRAPH": {
                     "samtools": "1.23.1"
@@ -109,6 +109,12 @@
                 "SAMTOOLS_SPLITHEADER": {
                     "samtools": "1.23.1"
                 },
+                "SAMTOOLS_SPLITHEADER_BAM": {
+                    "samtools": "1.23.1"
+                },
+                "SAMTOOLS_SPLITHEADER_EXTRA": {
+                    "samtools": "1.23.1"
+                },
                 "SAMTOOLS_STATS": {
                     "samtools": "1.23.1"
                 },
@@ -386,8 +392,8 @@
             {
                 "GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.bwamem2.cram": [
                     "@HD\tVN:1.6\tSO:coordinate",
-                    "@SQ\tSN:OV277441.1\tLN:7999920\tM5:0457acf8690429f1c98ee545cb8573b8\tUR:/nfs/treeoflife-01/<ABS_PATH>\tAS:GCA_922984935.2\tAN:SUPER_1\tSP:Meles meles",
-                    "@RG\tID:35528_2_1\tPL:ILLUMINA\tSM:SAMEA7524440",
+                    "@SQ\tSN:OV277441.1\tLN:7999920\tM5:0457acf8690429f1c98ee545cb8573b8\tUR:GCA_922984935.2.subset.fasta.gz\tAS:GCA_922984935.2\tAN:SUPER_1\tSP:Meles meles",
+                    "@RG\tID:35528_2#1\tDT:2020-11-17T00:00:00+0000\tPU:201117_A00948_0206_AHGML2DSXY_2#1\tLB:33637906\tPG:SCS\tSM:SAMEA5962964\tCN:SC\tPL:ILLUMINA\tDS:ERP116890: Sequencing and assembly of genomes from British species for the Darwin Tree of Life Project. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ ",
                     "@PG\tID:SCS.extra_header\tVN:1.7.0\tPN:NovaSeq Control Software\tDS:Controlling software on instrument",
                     "@PG\tID:basecalling.extra_header\tPP:SCS.extra_header\tVN:Unknown\tPN:Unknown\tDS:Basecalling Package",
                     "@PG\tID:bambi.extra_header\tPP:basecalling.extra_header\tVN:0.13.1\tCL:/software/pkgg/bambi/0.13.1/bin/bambi i2b --intensity-dir=/lustre/scratch121/esa-sv-20200210-01/IL_seq_data/analysis/201117_A00948_0206_AHGML2DSXY/Data/Intensities --basecalls-dir=/lustre/scratch121/esa-sv-20200210-01/IL_seq_data/analysis/201117_A00948_0206_AHGML2DSXY/Data/Intensities/BaseCalls --lane=2 --platform-unit=201117_A00948_0206_AHGML2DSXY_2 --read-group-id=35528_2 --study-name=\"ERP116890: Sequencing and assembly of genomes from British species for the Darwin Tree of Life Project. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ \" --sample-alias=SAMEA5962964,mCerEla1 --threads=8 --output-file=- --compression-level=0\tPN:bambi\tDS:Convert Illumina BCL to BAM or SAM file",
@@ -404,11 +410,11 @@
                     "@PG\tID:samtools.3.extra_header\tPN:samtools\tPP:scramble.extra_header\tVN:1.15\tCL:/usr/local/bin/samtools view -h /lustre/scratch124/tol/projects/darwin/data/mammals/Meles_meles/genomic_data/mMelMel3/hic-arima2/35528_2#1.cram",
                     "@PG\tID:samtools.4.extra_header\tPN:samtools\tPP:samtools.3.extra_header\tVN:1.20\tCL:/usr/local/bin/samtools view --cram 35528_2#1.subset.sam",
                     "@PG\tID:samtools.5.extra_header\tPN:samtools\tPP:samtools.4.extra_header\tVN:1.23.1\tCL:samtools view -H 35528_2_1.subset.cram",
-                    "@PG\tID:bwa-mem2\tPN:bwa-mem2\tVN:2.2.1\tCL:bwa-mem2 mem -5SPCp -t 4 ./bwamem2/GCA_922984935.2.subset.unmasked.fa -C -H @RG\\tID:35528_2_1\\tPL:ILLUMINA\\tSM:SAMEA7524440 -",
+                    "@PG\tID:bwa-mem2\tPN:bwa-mem2\tVN:2.2.1\tCL:bwa-mem2 mem -5SPCp -t 4 ./bwamem2/GCA_922984935.2.subset.unmasked.fa -C -H @RG\\tID:35528_2#1\\tDT:2020-11-17T00:00:00+0000\\tPU:201117_A00948_0206_AHGML2DSXY_2#1\\tLB:33637906\\tPG:SCS\\tSM:SAMEA5962964\\tCN:SC\\tPL:ILLUMINA\\tDS:ERP116890: Sequencing and assembly of genomes from British species for the Darwin Tree of Life Project. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/  -",
                     "@PG\tID:samtools\tPN:samtools\tPP:bwa-mem2\tVN:1.22.1\tCL:samtools fixmate -mpu - -",
                     "@PG\tID:samtools.1\tPN:samtools\tPP:samtools\tVN:1.22.1\tCL:samtools view -h",
-                    "@PG\tID:samtools.2\tPN:samtools\tPP:samtools.1\tVN:1.22.1\tCL:samtools sort --write-index -l1 -@4 -T 35528_2_1.subset_addRG.cram.0.SAMEA7524440.ERR6688402_tmp -o 35528_2_1.subset_addRG.cram.0.SAMEA7524440.ERR6688402.bam -",
-                    "@PG\tID:samtools.3\tPN:samtools\tPP:samtools.2\tVN:1.23.1\tCL:samtools merge --threads 3 -c -p --reference GCA_922984935.2.subset.unmasked.fa - 1/35528_2_1.subset_addRG.cram.0.SAMEA7524440.ERR6688402.bam 2/35528_2_1.subset_addRG.cram.1.SAMEA7524440.ERR6688402.bam",
+                    "@PG\tID:samtools.2\tPN:samtools\tPP:samtools.1\tVN:1.22.1\tCL:samtools sort --write-index -l1 -@4 -T 35528_2_1.subset.cram.0.SAMEA7524440.ERR6688402_tmp -o 35528_2_1.subset.cram.0.SAMEA7524440.ERR6688402.bam -",
+                    "@PG\tID:samtools.3\tPN:samtools\tPP:samtools.2\tVN:1.23.1\tCL:samtools merge --threads 3 -c -p --reference GCA_922984935.2.subset.unmasked.fa - 1/35528_2_1.subset.cram.0.SAMEA7524440.ERR6688402.bam 2/35528_2_1.subset.cram.1.SAMEA7524440.ERR6688402.bam",
                     "@PG\tID:samtools.4\tPN:samtools\tPP:samtools.3\tVN:1.23.1\tCL:samtools markdup -T SAMEA7524440.ERR6688402 -f SAMEA7524440.ERR6688402.metrics --threads 4 --reference GCA_922984935.2.subset.unmasked.fa - SAMEA7524440.ERR6688402.bam",
                     "@PG\tID:crumble\tPN:crumble\tPP:samtools.4\tVN:0.9.1\tCL:crumble -O bam SAMEA7524440.ERR6688402.bam SAMEA7524440.ERR6688402.crumble.bam",
                     "@PG\tID:samtools.5\tPN:samtools\tPP:samtools.5.extra_header\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.bwamem2.bam",
@@ -420,8 +426,8 @@
                 ],
                 "GCA_922984935.2.subset.illumina.SAMEA7524438.ERR6688599.bwamem2.cram": [
                     "@HD\tVN:1.6\tSO:coordinate",
-                    "@SQ\tSN:OV277441.1\tLN:7999920\tM5:0457acf8690429f1c98ee545cb8573b8\tUR:/nfs/treeoflife-01/<ABS_PATH>\tAS:GCA_922984935.2\tAN:SUPER_1\tSP:Meles meles",
-                    "@RG\tID:31231_3#1\tDT:2019-10-03T01:00:00+0100\tPU:191003_HX4_31231_A_H3353CCX2_3#1\tLB:23687379\tPG:SCS\tSM:SAMEA5962962\tCN:SC\tPL:ILLUMINA\tDS:ERP114452: Sequencing and assembly of vertebrate genomes from British species for the Darwin Tree of Life Project in collaboration with the Vertebrate Genomes Project. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",
+                    "@SQ\tSN:OV277441.1\tLN:7999920\tM5:0457acf8690429f1c98ee545cb8573b8\tUR:GCA_922984935.2.subset.fasta.gz\tAS:GCA_922984935.2\tAN:SUPER_1\tSP:Meles meles",
+                    "@RG\tID:31231_3#1\tDT:2019-10-03T00:00:00+0000\tPU:191003_HX4_31231_A_H3353CCX2_3#1\tLB:23687379\tPG:SCS\tSM:SAMEA5962962\tCN:SC\tPL:ILLUMINA\tDS:ERP114452: Sequencing and assembly of vertebrate genomes from British species for the Darwin Tree of Life Project in collaboration with the Vertebrate Genomes Project. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",
                     "@PG\tID:bwa-mem2\tPN:bwa-mem2\tVN:2.2.1\tCL:bwa-mem2 mem -p -t 4 ./bwamem2/GCA_922984935.2.subset.unmasked.fa -C -H @RG\\tID:31231_3#1\\tDT:2019-10-03T00:00:00+0000\\tPU:191003_HX4_31231_A_H3353CCX2_3#1\\tLB:23687379\\tPG:SCS\\tSM:SAMEA5962962\\tCN:SC\\tPL:ILLUMINA\\tDS:ERP114452: Sequencing and assembly of vertebrate genomes from British species for the Darwin Tree of Life Project in collaboration with the Vertebrate Genomes Project. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ -",
                     "@PG\tID:samtools\tPN:samtools\tPP:bwa-mem2\tVN:1.22.1\tCL:samtools fixmate -mpu - -",
                     "@PG\tID:samtools.1\tPN:samtools\tPP:samtools\tVN:1.22.1\tCL:samtools view -h",
@@ -434,7 +440,7 @@
                 ],
                 "GCA_922984935.2.subset.illumina.SAMEA7524439.ERR6688600.bwamem2.cram": [
                     "@HD\tVN:1.6\tSO:coordinate",
-                    "@SQ\tSN:OV277441.1\tLN:7999920\tM5:0457acf8690429f1c98ee545cb8573b8\tUR:/nfs/treeoflife-01/<ABS_PATH>\tAS:GCA_922984935.2\tAN:SUPER_1\tSP:Meles meles",
+                    "@SQ\tSN:OV277441.1\tLN:7999920\tM5:0457acf8690429f1c98ee545cb8573b8\tUR:GCA_922984935.2.subset.fasta.gz\tAS:GCA_922984935.2\tAN:SUPER_1\tSP:Meles meles",
                     "@RG\tID:31231_4_1\tPL:ILLUMINA\tSM:SAMEA7524439",
                     "@PG\tID:bwa-mem2\tPN:bwa-mem2\tVN:2.2.1\tCL:bwa-mem2 mem -p -t 4 ./bwamem2/GCA_922984935.2.subset.unmasked.fa -C -H @RG\\tID:31231_4_1\\tPL:ILLUMINA\\tSM:SAMEA7524439 -",
                     "@PG\tID:samtools\tPN:samtools\tPP:bwa-mem2\tVN:1.22.1\tCL:samtools fixmate -mpu - -",
@@ -448,7 +454,7 @@
                 ],
                 "GCA_922984935.2.subset.ont.SAMEA7524440.PAE35587.minimap2.cram": [
                     "@HD\tVN:1.6\tSO:coordinate",
-                    "@SQ\tSN:OV277441.1\tLN:7999920\tM5:0457acf8690429f1c98ee545cb8573b8\tUR:/nfs/treeoflife-01/<ABS_PATH>\tAS:GCA_922984935.2\tAN:SUPER_1\tSP:Meles meles",
+                    "@SQ\tSN:OV277441.1\tLN:7999920\tM5:0457acf8690429f1c98ee545cb8573b8\tUR:GCA_922984935.2.subset.fasta.gz\tAS:GCA_922984935.2\tAN:SUPER_1\tSP:Meles meles",
                     "@RG\tID:PAE35587_pass_1f1f0707_115\tPL:ONT\tSM:SAMEA7524440",
                     "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t4 -ax map-ont -y -R @RG\\tID:PAE35587_pass_1f1f0707_115\\tPL:ONT\\tSM:SAMEA7524440 -I1G -a GCA_922984935.2.subset.unmasked.mmi -",
                     "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.23.1\tCL:samtools sort -@ 3 -o PAE35587_pass_1f1f0707_115.subset.fastq.gz.0.SAMEA7524440.PAE35587.bam -T PAE35587_pass_1f1f0707_115.subset.fastq.gz.0.SAMEA7524440.PAE35587_sort_tmp --write-index -l1 -",
@@ -458,7 +464,7 @@
                 ],
                 "GCA_922984935.2.subset.ont.SAMEA7524440.PAE35587_test.minimap2.cram": [
                     "@HD\tVN:1.6\tSO:coordinate",
-                    "@SQ\tSN:OV277441.1\tLN:7999920\tM5:0457acf8690429f1c98ee545cb8573b8\tUR:/nfs/treeoflife-01/<ABS_PATH>\tAS:GCA_922984935.2\tAN:SUPER_1\tSP:Meles meles",
+                    "@SQ\tSN:OV277441.1\tLN:7999920\tM5:0457acf8690429f1c98ee545cb8573b8\tUR:GCA_922984935.2.subset.fasta.gz\tAS:GCA_922984935.2\tAN:SUPER_1\tSP:Meles meles",
                     "@RG\tID:PAE35587_pass_1f1f0707_115\tPL:ONT\tSM:mMelMel3",
                     "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t4 -ax map-ont -y -R @RG\\tID:PAE35587_pass_1f1f0707_115\\tPL:ONT\\tSM:mMelMel3 -I1G -a GCA_922984935.2.subset.unmasked.mmi -",
                     "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.23.1\tCL:samtools sort -@ 3 -o SAMEA7524440.PAE35587_test_other.fastq.gz.0.SAMEA7524440.PAE35587_test.bam -T SAMEA7524440.PAE35587_test_other.fastq.gz.0.SAMEA7524440.PAE35587_test_sort_tmp --write-index -l1 -",
@@ -468,7 +474,7 @@
                 ],
                 "GCA_922984935.2.subset.ont.SAMEA7524440.merged_1.minimap2.cram": [
                     "@HD\tVN:1.6\tSO:coordinate",
-                    "@SQ\tSN:OV277441.1\tLN:7999920\tM5:0457acf8690429f1c98ee545cb8573b8\tUR:/nfs/treeoflife-01/<ABS_PATH>\tAS:GCA_922984935.2\tAN:SUPER_1\tSP:Meles meles",
+                    "@SQ\tSN:OV277441.1\tLN:7999920\tM5:0457acf8690429f1c98ee545cb8573b8\tUR:GCA_922984935.2.subset.fasta.gz\tAS:GCA_922984935.2\tAN:SUPER_1\tSP:Meles meles",
                     "@RG\tID:PAE35587_pass_1f1f0707_115\tPL:ONT\tSM:SAMEA7524440",
                     "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t4 -ax map-ont -y -R @RG\\tID:PAE35587_pass_1f1f0707_115\\tPL:ONT\\tSM:SAMEA7524440 -I1G -a GCA_922984935.2.subset.unmasked.mmi -",
                     "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.23.1\tCL:samtools sort -@ 3 -o PAE35587_pass_1f1f0707_115.subset.fastq.gz.0.SAMEA7524440.PAE35587.bam -T PAE35587_pass_1f1f0707_115.subset.fastq.gz.0.SAMEA7524440.PAE35587_sort_tmp --write-index -l1 -",
@@ -479,7 +485,7 @@
                 ],
                 "GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939248.minimap2.cram": [
                     "@HD\tVN:1.6\tSO:coordinate",
-                    "@SQ\tSN:OV277441.1\tLN:7999920\tM5:0457acf8690429f1c98ee545cb8573b8\tUR:/nfs/treeoflife-01/<ABS_PATH>\tAS:GCA_922984935.2\tAN:SUPER_1\tSP:Meles meles",
+                    "@SQ\tSN:OV277441.1\tLN:7999920\tM5:0457acf8690429f1c98ee545cb8573b8\tUR:GCA_922984935.2.subset.fasta.gz\tAS:GCA_922984935.2\tAN:SUPER_1\tSP:Meles meles",
                     "@RG\tID:61ddc6c3/15--15\tPL:PACBIO\tDS:READTYPE=CCS;BINDINGKIT=101-789-500;SEQUENCINGKIT=101-826-100;BASECALLERVERSION=5.0.0;FRAMERATEHZ=100.000000;BarcodeFile=/lustre/scratch116/vr/projects/vgp/ref/barcodes/Sequel_16_Barcodes_v3.fasta;BarcodeHash=e418d89cefcbef90f3cb0e6455b7e2a3;BarcodeCount=16;BarcodeMode=Symmetric;BarcodeQuality=Score\tLB:DN615654G-A1\tPU:m64094_200910_173211\tPM:SEQUELII\tBC:CACTCACGTGTGATATT\tCM:S/P4-C2/5.0-8M\tSM:SAMEA7524440",
                     "@PG\tID:ccs-4.2.0.extra_header\tPN:ccs\tVN:4.2.0\tDS:Generate circular consensus sequences (ccs) from subreads.\tCL:ccs ccs --chunk 1/64 -j 8 --max-length 50000 ../../m64094_200910_173211.subreads.bam m64094_200910_173211.ccs.bam",
                     "@PG\tID:lima.extra_header\tVN:1.11.0 (commit v1.11.0)\tCL:lima -j 8 --split-bam-named --same --peek-guess --guess-min-count 1000 --ccs m64094_200910_173211.ccs.bam /lustre/scratch116/vr/projects/vgp/ref/barcodes/Sequel_16_Barcodes_v3.fasta lima/m64094_200910_173211.ccs.bam",
@@ -499,18 +505,17 @@
                 ],
                 "GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.cram": [
                     "@HD\tVN:1.6\tSO:coordinate",
-                    "@SQ\tSN:OV277441.1\tLN:7999920\tM5:0457acf8690429f1c98ee545cb8573b8\tUR:/nfs/treeoflife-01/<ABS_PATH>\tAS:GCA_922984935.2\tAN:SUPER_1\tSP:Meles meles",
-                    "@RG\tID:m64094_200911_174739\tPL:PACBIO\tSM:SAMEA7524440",
-                    "@PG\tID:samtools.extra_header\tPN:samtools\tVN:1.22.1\tCL:samtools collate --output-fmt cram -O -u -T mMelMel3_T4.collate --threads 4 --reference GCA_922984935.2.subset.unmasked.fasta m64094_200911_174739.ccs.bc1022_BAK8B_OA--bc1022_BAK8B_OA.subset.fastq.gz -",
-                    "@PG\tID:samtools.1.extra_header\tPN:samtools\tPP:samtools.extra_header\tVN:1.22.1\tCL:samtools fixmate -m -u --threads 4 - -",
-                    "@PG\tID:samtools.2.extra_header\tPN:samtools\tPP:samtools.1.extra_header\tVN:1.22.1\tCL:samtools sort -u -T mMelMel3_T4.sort --threads 4 -",
-                    "@PG\tID:samtools.3.extra_header\tPN:samtools\tPP:samtools.2.extra_header\tVN:1.22.1\tCL:samtools markdup -T mMelMel3_T4.markdup -f mMelMel3_T4.metrics --threads 4 - mMelMel3_T4.cram",
-                    "@PG\tID:samtools.4.extra_header\tPN:samtools\tPP:samtools.3.extra_header\tVN:1.23.1\tCL:samtools view -H m64094_200911_174739.ccs.bc1022_BAK8B_OA--bc1022_BAK8B_OA.subset.cram",
-                    "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t4 -ax map-hifi --cs=short -y -R @RG\\tID:m64094_200911_174739\\tPL:PACBIO\\tSM:SAMEA7524440 -I1G -a GCA_922984935.2.subset.unmasked.mmi -",
+                    "@SQ\tSN:OV277441.1\tLN:7999920\tM5:0457acf8690429f1c98ee545cb8573b8\tUR:GCA_922984935.2.subset.fasta.gz\tAS:GCA_922984935.2\tAN:SUPER_1\tSP:Meles meles",
+                    "@RG\tID:aaa0cf18/15--15\tPL:PACBIO\tDS:READTYPE=CCS;BINDINGKIT=101-789-500;SEQUENCINGKIT=101-826-100;BASECALLERVERSION=5.0.0;FRAMERATEHZ=100.000000;BarcodeFile=/lustre/scratch116/vr/projects/vgp/ref/barcodes/Sequel_16_Barcodes_v3.fasta;BarcodeHash=e418d89cefcbef90f3cb0e6455b7e2a3;BarcodeCount=16;BarcodeMode=Symmetric;BarcodeQuality=Score\tLB:DN615654G-A1\tPU:m64094_200911_174739\tPM:SEQUELII\tBC:CACTCACGTGTGATATT\tCM:S/P4-C2/5.0-8M\tSM:SAMEA7524440",
+                    "@PG\tID:ccs-4.2.0.extra_header\tPN:ccs\tVN:4.2.0\tDS:Generate circular consensus sequences (ccs) from subreads.\tCL:ccs ccs --chunk 1/64 -j 8 --max-length 50000 ../../m64094_200911_174739.subreads.bam m64094_200911_174739.ccs.bam",
+                    "@PG\tID:lima.extra_header\tVN:1.11.0 (commit v1.11.0)\tCL:lima -j 8 --split-bam-named --same --peek-guess --guess-min-count 1000 --ccs m64094_200911_174739.ccs.bam /lustre/scratch116/vr/projects/vgp/ref/barcodes/Sequel_16_Barcodes_v3.fasta lima/m64094_200911_174739.ccs.bam",
+                    "@PG\tID:samtools.extra_header\tPN:samtools\tVN:1.10\tPP:ccs-4.2.0.extra_header\tCL:samtools merge -@8 -ncp -b m64094_200911_174739.chunks.fofn m64094_200911_174739.ccs.bam",
+                    "@PG\tID:samtools.1.extra_header\tPN:samtools\tPP:samtools.extra_header\tVN:1.23.1\tCL:samtools view -H /lustre/scratch122/tol/data/9/9/f/1/6/d/Meles_meles/genomic_data/mMelMel3/pacbio/m64094_200911_174739.ccs.bc1022_BAK8B_OA--bc1022_BAK8B_OA.bam",
+                    "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t4 -ax map-hifi --cs=short -y -R @RG\\tID:aaa0cf18/15--15\\tPL:PACBIO\\tDS:READTYPE=CCS;BINDINGKIT=101-789-500;SEQUENCINGKIT=101-826-100;BASECALLERVERSION=5.0.0;FRAMERATEHZ=100.000000;BarcodeFile=/lustre/scratch116/vr/projects/vgp/ref/barcodes/Sequel_16_Barcodes_v3.fasta;BarcodeHash=e418d89cefcbef90f3cb0e6455b7e2a3;BarcodeCount=16;BarcodeMode=Symmetric;BarcodeQuality=Score\\tLB:DN615654G-A1\\tPU:m64094_200911_174739\\tPM:SEQUELII\\tBC:CACTCACGTGTGATATT\\tCM:S/P4-C2/5.0-8M\\tSM:SAMEA7524440 -I1G -a GCA_922984935.2.subset.unmasked.mmi -",
                     "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.23.1\tCL:samtools sort -@ 3 -o pacbio.SAMEA7524440.ERR6939249.hifitrimmer.fastq.gz.0.SAMEA7524440.ERR6939249.bam -T pacbio.SAMEA7524440.ERR6939249.hifitrimmer.fastq.gz.0.SAMEA7524440.ERR6939249_sort_tmp --write-index -l1 -",
                     "@PG\tID:samtools.1\tPN:samtools\tPP:samtools\tVN:1.23.1\tCL:samtools merge --threads 3 -c -p --reference GCA_922984935.2.subset.unmasked.fa SAMEA7524440.ERR6939249.merge.bam 1/pacbio.SAMEA7524440.ERR6939249.hifitrimmer.fastq.gz.0.SAMEA7524440.ERR6939249.bam",
                     "@PG\tID:crumble\tPN:crumble\tPP:samtools.1\tVN:0.9.1\tCL:crumble -y pbccs -O bam SAMEA7524440.ERR6939249.merge.bam SAMEA7524440.ERR6939249.merge.crumble.bam",
-                    "@PG\tID:samtools.2\tPN:samtools\tPP:samtools.4.extra_header\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.bam",
+                    "@PG\tID:samtools.2\tPN:samtools\tPP:samtools.1.extra_header\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.bam",
                     "@PG\tID:samtools.3\tPN:samtools\tPP:crumble\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.bam",
                     "@PG\tID:samtools.4\tPN:samtools\tPP:samtools.2\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1 --write-index -o GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.cram GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.bam",
                     "@PG\tID:samtools.5\tPN:samtools\tPP:samtools.3\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1 --write-index -o GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.cram GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.bam",
@@ -519,9 +524,9 @@
                 ],
                 "GCA_922984935.2.subset.pacbio.SAMEA7524440.merged_1.minimap2.cram": [
                     "@HD\tVN:1.6\tSO:coordinate",
-                    "@SQ\tSN:OV277441.1\tLN:7999920\tM5:0457acf8690429f1c98ee545cb8573b8\tUR:/nfs/treeoflife-01/<ABS_PATH>\tAS:GCA_922984935.2\tAN:SUPER_1\tSP:Meles meles",
+                    "@SQ\tSN:OV277441.1\tLN:7999920\tM5:0457acf8690429f1c98ee545cb8573b8\tUR:GCA_922984935.2.subset.fasta.gz\tAS:GCA_922984935.2\tAN:SUPER_1\tSP:Meles meles",
                     "@RG\tID:61ddc6c3/15--15\tPL:PACBIO\tDS:READTYPE=CCS;BINDINGKIT=101-789-500;SEQUENCINGKIT=101-826-100;BASECALLERVERSION=5.0.0;FRAMERATEHZ=100.000000;BarcodeFile=/lustre/scratch116/vr/projects/vgp/ref/barcodes/Sequel_16_Barcodes_v3.fasta;BarcodeHash=e418d89cefcbef90f3cb0e6455b7e2a3;BarcodeCount=16;BarcodeMode=Symmetric;BarcodeQuality=Score\tLB:DN615654G-A1\tPU:m64094_200910_173211\tPM:SEQUELII\tBC:CACTCACGTGTGATATT\tCM:S/P4-C2/5.0-8M\tSM:SAMEA7524440",
-                    "@RG\tID:m64094_200911_174739\tPL:PACBIO\tSM:SAMEA7524440",
+                    "@RG\tID:aaa0cf18/15--15\tPL:PACBIO\tDS:READTYPE=CCS;BINDINGKIT=101-789-500;SEQUENCINGKIT=101-826-100;BASECALLERVERSION=5.0.0;FRAMERATEHZ=100.000000;BarcodeFile=/lustre/scratch116/vr/projects/vgp/ref/barcodes/Sequel_16_Barcodes_v3.fasta;BarcodeHash=e418d89cefcbef90f3cb0e6455b7e2a3;BarcodeCount=16;BarcodeMode=Symmetric;BarcodeQuality=Score\tLB:DN615654G-A1\tPU:m64094_200911_174739\tPM:SEQUELII\tBC:CACTCACGTGTGATATT\tCM:S/P4-C2/5.0-8M\tSM:SAMEA7524440",
                     "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t4 -ax map-hifi --cs=short -y -R @RG\\tID:61ddc6c3/15--15\\tPL:PACBIO\\tDS:READTYPE=CCS;BINDINGKIT=101-789-500;SEQUENCINGKIT=101-826-100;BASECALLERVERSION=5.0.0;FRAMERATEHZ=100.000000;BarcodeFile=/lustre/scratch116/vr/projects/vgp/ref/barcodes/Sequel_16_Barcodes_v3.fasta;BarcodeHash=e418d89cefcbef90f3cb0e6455b7e2a3;BarcodeCount=16;BarcodeMode=Symmetric;BarcodeQuality=Score\\tLB:DN615654G-A1\\tPU:m64094_200910_173211\\tPM:SEQUELII\\tBC:CACTCACGTGTGATATT\\tCM:S/P4-C2/5.0-8M\\tSM:SAMEA7524440 -I1G -a GCA_922984935.2.subset.unmasked.mmi -",
                     "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.23.1\tCL:samtools sort -@ 3 -o pacbio.SAMEA7524440.ERR6939248.hifitrimmer.fastq.gz.0.SAMEA7524440.ERR6939248.bam -T pacbio.SAMEA7524440.ERR6939248.hifitrimmer.fastq.gz.0.SAMEA7524440.ERR6939248_sort_tmp --write-index -l1 -",
                     "@PG\tID:samtools.1\tPN:samtools\tPP:samtools\tVN:1.23.1\tCL:samtools merge --threads 3 -c -p --reference GCA_922984935.2.subset.unmasked.fa SAMEA7524440.ERR6939248.merge.bam 1/pacbio.SAMEA7524440.ERR6939248.hifitrimmer.fastq.gz.0.SAMEA7524440.ERR6939248.bam",
@@ -540,6 +545,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.4"
         },
-        "timestamp": "2026-05-29T03:22:38.8477332"
+        "timestamp": "2026-06-03T16:06:47.981156535"
     }
 }
\ No newline at end of file
diff --git a/tests/short_aligner_minimap2.nf.test.snap b/tests/short_aligner_minimap2.nf.test.snap
index 9d955622..fcf979ae 100644
--- a/tests/short_aligner_minimap2.nf.test.snap
+++ b/tests/short_aligner_minimap2.nf.test.snap
@@ -82,6 +82,12 @@
                 "SAMTOOLS_SPLITHEADER": {
                     "samtools": "1.23.1"
                 },
+                "SAMTOOLS_SPLITHEADER_BAM": {
+                    "samtools": "1.23.1"
+                },
+                "SAMTOOLS_SPLITHEADER_EXTRA": {
+                    "samtools": "1.23.1"
+                },
                 "SAMTOOLS_STATS": {
                     "samtools": "1.23.1"
                 },
@@ -226,8 +232,8 @@
             {
                 "GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.minimap2.bam": [
                     "@HD\tVN:1.6\tSO:coordinate",
-                    "@SQ\tSN:OV277441.1\tLN:7999920\tM5:0457acf8690429f1c98ee545cb8573b8\tUR:/nfs/treeoflife-01/<ABS_PATH>\tAS:GCA_922984935.2\tAN:SUPER_1\tSP:Meles meles",
-                    "@RG\tID:35528_2_1\tPL:ILLUMINA\tSM:SAMEA7524440",
+                    "@SQ\tSN:OV277441.1\tLN:7999920\tM5:0457acf8690429f1c98ee545cb8573b8\tUR:GCA_922984935.2.subset.fasta.gz\tAS:GCA_922984935.2\tAN:SUPER_1\tSP:Meles meles",
+                    "@RG\tID:35528_2#1\tDT:2020-11-17T00:00:00+0000\tPU:201117_A00948_0206_AHGML2DSXY_2#1\tLB:33637906\tPG:SCS\tSM:SAMEA5962964\tCN:SC\tPL:ILLUMINA\tDS:ERP116890: Sequencing and assembly of genomes from British species for the Darwin Tree of Life Project. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ ",
                     "@PG\tID:SCS.extra_header\tVN:1.7.0\tPN:NovaSeq Control Software\tDS:Controlling software on instrument",
                     "@PG\tID:basecalling.extra_header\tPP:SCS.extra_header\tVN:Unknown\tPN:Unknown\tDS:Basecalling Package",
                     "@PG\tID:bambi.extra_header\tPP:basecalling.extra_header\tVN:0.13.1\tCL:/software/pkgg/bambi/0.13.1/bin/bambi i2b --intensity-dir=/lustre/scratch121/esa-sv-20200210-01/IL_seq_data/analysis/201117_A00948_0206_AHGML2DSXY/Data/Intensities --basecalls-dir=/lustre/scratch121/esa-sv-20200210-01/IL_seq_data/analysis/201117_A00948_0206_AHGML2DSXY/Data/Intensities/BaseCalls --lane=2 --platform-unit=201117_A00948_0206_AHGML2DSXY_2 --read-group-id=35528_2 --study-name=\"ERP116890: Sequencing and assembly of genomes from British species for the Darwin Tree of Life Project. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ \" --sample-alias=SAMEA5962964,mCerEla1 --threads=8 --output-file=- --compression-level=0\tPN:bambi\tDS:Convert Illumina BCL to BAM or SAM file",
@@ -244,11 +250,11 @@
                     "@PG\tID:samtools.3.extra_header\tPN:samtools\tPP:scramble.extra_header\tVN:1.15\tCL:/usr/local/bin/samtools view -h /lustre/scratch124/tol/projects/darwin/data/mammals/Meles_meles/genomic_data/mMelMel3/hic-arima2/35528_2#1.cram",
                     "@PG\tID:samtools.4.extra_header\tPN:samtools\tPP:samtools.3.extra_header\tVN:1.20\tCL:/usr/local/bin/samtools view --cram 35528_2#1.subset.sam",
                     "@PG\tID:samtools.5.extra_header\tPN:samtools\tPP:samtools.4.extra_header\tVN:1.23.1\tCL:samtools view -H 35528_2_1.subset.cram",
-                    "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t4 -ax sr --cs=short -I1.0G -y -R @RG\\tID:35528_2_1\\tPL:ILLUMINA\\tSM:SAMEA7524440 GCA_922984935.2.subset.unmasked.mmi -",
+                    "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t4 -ax sr --cs=short -I1.0G -y -R @RG\\tID:35528_2#1\\tDT:2020-11-17T00:00:00+0000\\tPU:201117_A00948_0206_AHGML2DSXY_2#1\\tLB:33637906\\tPG:SCS\\tSM:SAMEA5962964\\tCN:SC\\tPL:ILLUMINA\\tDS:ERP116890: Sequencing and assembly of genomes from British species for the Darwin Tree of Life Project. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/  GCA_922984935.2.subset.unmasked.mmi -",
                     "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.22.1\tCL:samtools fixmate -mpu - -",
                     "@PG\tID:samtools.1\tPN:samtools\tPP:samtools\tVN:1.22.1\tCL:samtools view -h",
-                    "@PG\tID:samtools.2\tPN:samtools\tPP:samtools.1\tVN:1.22.1\tCL:samtools sort --write-index -l1 -@4 -T 35528_2_1.subset_addRG.cram.0.SAMEA7524440.ERR6688402_tmp -o 35528_2_1.subset_addRG.cram.0.SAMEA7524440.ERR6688402.bam -",
-                    "@PG\tID:samtools.3\tPN:samtools\tPP:samtools.2\tVN:1.23.1\tCL:samtools merge --threads 3 -c -p --reference GCA_922984935.2.subset.unmasked.fa - 1/35528_2_1.subset_addRG.cram.0.SAMEA7524440.ERR6688402.bam 2/35528_2_1.subset_addRG.cram.1.SAMEA7524440.ERR6688402.bam",
+                    "@PG\tID:samtools.2\tPN:samtools\tPP:samtools.1\tVN:1.22.1\tCL:samtools sort --write-index -l1 -@4 -T 35528_2_1.subset.cram.0.SAMEA7524440.ERR6688402_tmp -o 35528_2_1.subset.cram.0.SAMEA7524440.ERR6688402.bam -",
+                    "@PG\tID:samtools.3\tPN:samtools\tPP:samtools.2\tVN:1.23.1\tCL:samtools merge --threads 3 -c -p --reference GCA_922984935.2.subset.unmasked.fa - 1/35528_2_1.subset.cram.0.SAMEA7524440.ERR6688402.bam 2/35528_2_1.subset.cram.1.SAMEA7524440.ERR6688402.bam",
                     "@PG\tID:samtools.4\tPN:samtools\tPP:samtools.3\tVN:1.23.1\tCL:samtools markdup -T SAMEA7524440.ERR6688402 -f SAMEA7524440.ERR6688402.metrics --threads 4 --reference GCA_922984935.2.subset.unmasked.fa - SAMEA7524440.ERR6688402.bam",
                     "@PG\tID:crumble\tPN:crumble\tPP:samtools.4\tVN:0.9.1\tCL:crumble -O bam SAMEA7524440.ERR6688402.bam SAMEA7524440.ERR6688402.crumble.bam",
                     "@PG\tID:samtools.5\tPN:samtools\tPP:samtools.5.extra_header\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.minimap2.bam",
@@ -258,8 +264,8 @@
                 ],
                 "GCA_922984935.2.subset.illumina.SAMEA7524438.ERR6688599.minimap2.bam": [
                     "@HD\tVN:1.6\tSO:coordinate",
-                    "@SQ\tSN:OV277441.1\tLN:7999920\tM5:0457acf8690429f1c98ee545cb8573b8\tUR:/nfs/treeoflife-01/<ABS_PATH>\tAS:GCA_922984935.2\tAN:SUPER_1\tSP:Meles meles",
-                    "@RG\tID:31231_3#1\tPU:191003_HX4_31231_A_H3353CCX2_3#1\tLB:23687379\tPG:SCS\tSM:SAMEA5962962\tCN:SC\tPL:ILLUMINA\tDS:ERP114452: Sequencing and assembly of vertebrate genomes from British species for the Darwin Tree of Life Project in collaboration with the Vertebrate Genomes Project. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",
+                    "@SQ\tSN:OV277441.1\tLN:7999920\tM5:0457acf8690429f1c98ee545cb8573b8\tUR:GCA_922984935.2.subset.fasta.gz\tAS:GCA_922984935.2\tAN:SUPER_1\tSP:Meles meles",
+                    "@RG\tID:31231_3#1\tDT:2019-10-03T00:00:00+0000\tPU:191003_HX4_31231_A_H3353CCX2_3#1\tLB:23687379\tPG:SCS\tSM:SAMEA5962962\tCN:SC\tPL:ILLUMINA\tDS:ERP114452: Sequencing and assembly of vertebrate genomes from British species for the Darwin Tree of Life Project in collaboration with the Vertebrate Genomes Project. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",
                     "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t4 -ax sr --cs=short -I1.0G -y -R @RG\\tID:31231_3#1\\tDT:2019-10-03T00:00:00+0000\\tPU:191003_HX4_31231_A_H3353CCX2_3#1\\tLB:23687379\\tPG:SCS\\tSM:SAMEA5962962\\tCN:SC\\tPL:ILLUMINA\\tDS:ERP114452: Sequencing and assembly of vertebrate genomes from British species for the Darwin Tree of Life Project in collaboration with the Vertebrate Genomes Project. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ GCA_922984935.2.subset.unmasked.mmi -",
                     "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.22.1\tCL:samtools fixmate -mpu - -",
                     "@PG\tID:samtools.1\tPN:samtools\tPP:samtools\tVN:1.22.1\tCL:samtools view -h",
@@ -271,7 +277,7 @@
                 ],
                 "GCA_922984935.2.subset.illumina.SAMEA7524439.ERR6688600.minimap2.bam": [
                     "@HD\tVN:1.6\tSO:coordinate",
-                    "@SQ\tSN:OV277441.1\tLN:7999920\tM5:0457acf8690429f1c98ee545cb8573b8\tUR:/nfs/treeoflife-01/<ABS_PATH>\tAS:GCA_922984935.2\tAN:SUPER_1\tSP:Meles meles",
+                    "@SQ\tSN:OV277441.1\tLN:7999920\tM5:0457acf8690429f1c98ee545cb8573b8\tUR:GCA_922984935.2.subset.fasta.gz\tAS:GCA_922984935.2\tAN:SUPER_1\tSP:Meles meles",
                     "@RG\tID:31231_4_1\tPL:ILLUMINA\tSM:SAMEA7524439",
                     "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t4 -ax sr --cs=short -I1.0G -y -R @RG\\tID:31231_4_1\\tPL:ILLUMINA\\tSM:SAMEA7524439 GCA_922984935.2.subset.unmasked.mmi -",
                     "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.22.1\tCL:samtools fixmate -mpu - -",
@@ -286,8 +292,8 @@
             {
                 "GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.minimap2.cram": [
                     "@HD\tVN:1.6\tSO:coordinate",
-                    "@SQ\tSN:OV277441.1\tLN:7999920\tM5:0457acf8690429f1c98ee545cb8573b8\tUR:/nfs/treeoflife-01/<ABS_PATH>\tAS:GCA_922984935.2\tAN:SUPER_1\tSP:Meles meles",
-                    "@RG\tID:35528_2_1\tPL:ILLUMINA\tSM:SAMEA7524440",
+                    "@SQ\tSN:OV277441.1\tLN:7999920\tM5:0457acf8690429f1c98ee545cb8573b8\tUR:GCA_922984935.2.subset.fasta.gz\tAS:GCA_922984935.2\tAN:SUPER_1\tSP:Meles meles",
+                    "@RG\tID:35528_2#1\tDT:2020-11-17T00:00:00+0000\tPU:201117_A00948_0206_AHGML2DSXY_2#1\tLB:33637906\tPG:SCS\tSM:SAMEA5962964\tCN:SC\tPL:ILLUMINA\tDS:ERP116890: Sequencing and assembly of genomes from British species for the Darwin Tree of Life Project. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ ",
                     "@PG\tID:SCS.extra_header\tVN:1.7.0\tPN:NovaSeq Control Software\tDS:Controlling software on instrument",
                     "@PG\tID:basecalling.extra_header\tPP:SCS.extra_header\tVN:Unknown\tPN:Unknown\tDS:Basecalling Package",
                     "@PG\tID:bambi.extra_header\tPP:basecalling.extra_header\tVN:0.13.1\tCL:/software/pkgg/bambi/0.13.1/bin/bambi i2b --intensity-dir=/lustre/scratch121/esa-sv-20200210-01/IL_seq_data/analysis/201117_A00948_0206_AHGML2DSXY/Data/Intensities --basecalls-dir=/lustre/scratch121/esa-sv-20200210-01/IL_seq_data/analysis/201117_A00948_0206_AHGML2DSXY/Data/Intensities/BaseCalls --lane=2 --platform-unit=201117_A00948_0206_AHGML2DSXY_2 --read-group-id=35528_2 --study-name=\"ERP116890: Sequencing and assembly of genomes from British species for the Darwin Tree of Life Project. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ \" --sample-alias=SAMEA5962964,mCerEla1 --threads=8 --output-file=- --compression-level=0\tPN:bambi\tDS:Convert Illumina BCL to BAM or SAM file",
@@ -304,11 +310,11 @@
                     "@PG\tID:samtools.3.extra_header\tPN:samtools\tPP:scramble.extra_header\tVN:1.15\tCL:/usr/local/bin/samtools view -h /lustre/scratch124/tol/projects/darwin/data/mammals/Meles_meles/genomic_data/mMelMel3/hic-arima2/35528_2#1.cram",
                     "@PG\tID:samtools.4.extra_header\tPN:samtools\tPP:samtools.3.extra_header\tVN:1.20\tCL:/usr/local/bin/samtools view --cram 35528_2#1.subset.sam",
                     "@PG\tID:samtools.5.extra_header\tPN:samtools\tPP:samtools.4.extra_header\tVN:1.23.1\tCL:samtools view -H 35528_2_1.subset.cram",
-                    "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t4 -ax sr --cs=short -I1.0G -y -R @RG\\tID:35528_2_1\\tPL:ILLUMINA\\tSM:SAMEA7524440 GCA_922984935.2.subset.unmasked.mmi -",
+                    "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t4 -ax sr --cs=short -I1.0G -y -R @RG\\tID:35528_2#1\\tDT:2020-11-17T00:00:00+0000\\tPU:201117_A00948_0206_AHGML2DSXY_2#1\\tLB:33637906\\tPG:SCS\\tSM:SAMEA5962964\\tCN:SC\\tPL:ILLUMINA\\tDS:ERP116890: Sequencing and assembly of genomes from British species for the Darwin Tree of Life Project. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/  GCA_922984935.2.subset.unmasked.mmi -",
                     "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.22.1\tCL:samtools fixmate -mpu - -",
                     "@PG\tID:samtools.1\tPN:samtools\tPP:samtools\tVN:1.22.1\tCL:samtools view -h",
-                    "@PG\tID:samtools.2\tPN:samtools\tPP:samtools.1\tVN:1.22.1\tCL:samtools sort --write-index -l1 -@4 -T 35528_2_1.subset_addRG.cram.0.SAMEA7524440.ERR6688402_tmp -o 35528_2_1.subset_addRG.cram.0.SAMEA7524440.ERR6688402.bam -",
-                    "@PG\tID:samtools.3\tPN:samtools\tPP:samtools.2\tVN:1.23.1\tCL:samtools merge --threads 3 -c -p --reference GCA_922984935.2.subset.unmasked.fa - 1/35528_2_1.subset_addRG.cram.0.SAMEA7524440.ERR6688402.bam 2/35528_2_1.subset_addRG.cram.1.SAMEA7524440.ERR6688402.bam",
+                    "@PG\tID:samtools.2\tPN:samtools\tPP:samtools.1\tVN:1.22.1\tCL:samtools sort --write-index -l1 -@4 -T 35528_2_1.subset.cram.0.SAMEA7524440.ERR6688402_tmp -o 35528_2_1.subset.cram.0.SAMEA7524440.ERR6688402.bam -",
+                    "@PG\tID:samtools.3\tPN:samtools\tPP:samtools.2\tVN:1.23.1\tCL:samtools merge --threads 3 -c -p --reference GCA_922984935.2.subset.unmasked.fa - 1/35528_2_1.subset.cram.0.SAMEA7524440.ERR6688402.bam 2/35528_2_1.subset.cram.1.SAMEA7524440.ERR6688402.bam",
                     "@PG\tID:samtools.4\tPN:samtools\tPP:samtools.3\tVN:1.23.1\tCL:samtools markdup -T SAMEA7524440.ERR6688402 -f SAMEA7524440.ERR6688402.metrics --threads 4 --reference GCA_922984935.2.subset.unmasked.fa - SAMEA7524440.ERR6688402.bam",
                     "@PG\tID:crumble\tPN:crumble\tPP:samtools.4\tVN:0.9.1\tCL:crumble -O bam SAMEA7524440.ERR6688402.bam SAMEA7524440.ERR6688402.crumble.bam",
                     "@PG\tID:samtools.5\tPN:samtools\tPP:samtools.5.extra_header\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.minimap2.bam",
@@ -320,8 +326,8 @@
                 ],
                 "GCA_922984935.2.subset.illumina.SAMEA7524438.ERR6688599.minimap2.cram": [
                     "@HD\tVN:1.6\tSO:coordinate",
-                    "@SQ\tSN:OV277441.1\tLN:7999920\tM5:0457acf8690429f1c98ee545cb8573b8\tUR:/nfs/treeoflife-01/<ABS_PATH>\tAS:GCA_922984935.2\tAN:SUPER_1\tSP:Meles meles",
-                    "@RG\tID:31231_3#1\tPU:191003_HX4_31231_A_H3353CCX2_3#1\tLB:23687379\tPG:SCS\tSM:SAMEA5962962\tCN:SC\tPL:ILLUMINA\tDS:ERP114452: Sequencing and assembly of vertebrate genomes from British species for the Darwin Tree of Life Project in collaboration with the Vertebrate Genomes Project. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",
+                    "@SQ\tSN:OV277441.1\tLN:7999920\tM5:0457acf8690429f1c98ee545cb8573b8\tUR:GCA_922984935.2.subset.fasta.gz\tAS:GCA_922984935.2\tAN:SUPER_1\tSP:Meles meles",
+                    "@RG\tID:31231_3#1\tDT:2019-10-03T00:00:00+0000\tPU:191003_HX4_31231_A_H3353CCX2_3#1\tLB:23687379\tPG:SCS\tSM:SAMEA5962962\tCN:SC\tPL:ILLUMINA\tDS:ERP114452: Sequencing and assembly of vertebrate genomes from British species for the Darwin Tree of Life Project in collaboration with the Vertebrate Genomes Project. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",
                     "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t4 -ax sr --cs=short -I1.0G -y -R @RG\\tID:31231_3#1\\tDT:2019-10-03T00:00:00+0000\\tPU:191003_HX4_31231_A_H3353CCX2_3#1\\tLB:23687379\\tPG:SCS\\tSM:SAMEA5962962\\tCN:SC\\tPL:ILLUMINA\\tDS:ERP114452: Sequencing and assembly of vertebrate genomes from British species for the Darwin Tree of Life Project in collaboration with the Vertebrate Genomes Project. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ GCA_922984935.2.subset.unmasked.mmi -",
                     "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.22.1\tCL:samtools fixmate -mpu - -",
                     "@PG\tID:samtools.1\tPN:samtools\tPP:samtools\tVN:1.22.1\tCL:samtools view -h",
@@ -334,7 +340,7 @@
                 ],
                 "GCA_922984935.2.subset.illumina.SAMEA7524439.ERR6688600.minimap2.cram": [
                     "@HD\tVN:1.6\tSO:coordinate",
-                    "@SQ\tSN:OV277441.1\tLN:7999920\tM5:0457acf8690429f1c98ee545cb8573b8\tUR:/nfs/treeoflife-01/<ABS_PATH>\tAS:GCA_922984935.2\tAN:SUPER_1\tSP:Meles meles",
+                    "@SQ\tSN:OV277441.1\tLN:7999920\tM5:0457acf8690429f1c98ee545cb8573b8\tUR:GCA_922984935.2.subset.fasta.gz\tAS:GCA_922984935.2\tAN:SUPER_1\tSP:Meles meles",
                     "@RG\tID:31231_4_1\tPL:ILLUMINA\tSM:SAMEA7524439",
                     "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t4 -ax sr --cs=short -I1.0G -y -R @RG\\tID:31231_4_1\\tPL:ILLUMINA\\tSM:SAMEA7524439 GCA_922984935.2.subset.unmasked.mmi -",
                     "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.22.1\tCL:samtools fixmate -mpu - -",
@@ -355,6 +361,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.4"
         },
-        "timestamp": "2026-05-29T04:12:24.650580553"
+        "timestamp": "2026-06-03T15:03:31.017178618"
     }
 }
\ No newline at end of file
diff --git a/tests/uli.nf.test.snap b/tests/uli.nf.test.snap
index 31372cd3..67e31b7e 100644
--- a/tests/uli.nf.test.snap
+++ b/tests/uli.nf.test.snap
@@ -78,7 +78,7 @@
                 "SAMTOOLS_MERGE": {
                     "samtools": "1.23.1"
                 },
-                "SAMTOOLS_SPLITHEADER": {
+                "SAMTOOLS_SPLITHEADER_BAM": {
                     "samtools": "1.23.1"
                 },
                 "SAMTOOLS_STATS": {
@@ -209,6 +209,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.4"
         },
-        "timestamp": "2026-05-29T03:53:26.611534435"
+        "timestamp": "2026-06-03T15:10:45.578688714"
     }
 }
\ No newline at end of file
diff --git a/tests/uli_no_lima.nf.test.snap b/tests/uli_no_lima.nf.test.snap
index ab978f72..ae7ad0e0 100644
--- a/tests/uli_no_lima.nf.test.snap
+++ b/tests/uli_no_lima.nf.test.snap
@@ -75,7 +75,7 @@
                 "SAMTOOLS_MERGE": {
                     "samtools": "1.23.1"
                 },
-                "SAMTOOLS_SPLITHEADER": {
+                "SAMTOOLS_SPLITHEADER_BAM": {
                     "samtools": "1.23.1"
                 },
                 "SAMTOOLS_STATS": {
@@ -202,6 +202,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.4"
         },
-        "timestamp": "2026-05-28T20:23:05.002283734"
+        "timestamp": "2026-06-03T15:01:25.398827197"
     }
 }
\ No newline at end of file
diff --git a/tests/untrim.nf.test.snap b/tests/untrim.nf.test.snap
index 1b98a7cb..359723b2 100644
--- a/tests/untrim.nf.test.snap
+++ b/tests/untrim.nf.test.snap
@@ -63,7 +63,10 @@
                 "SAMTOOLS_REHEADER_BAM": {
                     "samtools": "1.23.1"
                 },
-                "SAMTOOLS_SPLITHEADER": {
+                "SAMTOOLS_SPLITHEADER_BAM": {
+                    "samtools": "1.23.1"
+                },
+                "SAMTOOLS_SPLITHEADER_EXTRA": {
                     "samtools": "1.23.1"
                 },
                 "SAMTOOLS_STATS": {
@@ -200,7 +203,7 @@
             {
                 "GCA_922984935.2.subset.ont.SAMEA7524440.PAE35587.minimap2.bam": [
                     "@HD\tVN:1.6\tSO:coordinate",
-                    "@SQ\tSN:OV277441.1\tLN:7999920\tM5:0457acf8690429f1c98ee545cb8573b8\tUR:/nfs/treeoflife-01/resources/<ABS_PATH>\tAS:GCA_922984935.2\tAN:SUPER_1\tSP:Meles meles",
+                    "@SQ\tSN:OV277441.1\tLN:7999920\tM5:0457acf8690429f1c98ee545cb8573b8\tUR:GCA_922984935.2.subset.fasta.gz\tAS:GCA_922984935.2\tAN:SUPER_1\tSP:Meles meles",
                     "@RG\tID:PAE35587_pass_1f1f0707_115\tPL:ONT\tSM:SAMEA7524440",
                     "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t4 -ax map-ont -y -R @RG\\tID:PAE35587_pass_1f1f0707_115\\tPL:ONT\\tSM:SAMEA7524440 -I1G -a GCA_922984935.2.subset.unmasked.mmi -",
                     "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.23.1\tCL:samtools sort -@ 3 -o PAE35587_pass_1f1f0707_115.subset.fastq.gz.0.SAMEA7524440.PAE35587.bam -T PAE35587_pass_1f1f0707_115.subset.fastq.gz.0.SAMEA7524440.PAE35587_sort_tmp --write-index -l1 -",
@@ -209,7 +212,7 @@
                 ],
                 "GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939248.minimap2.bam": [
                     "@HD\tVN:1.6\tSO:coordinate",
-                    "@SQ\tSN:OV277441.1\tLN:7999920\tM5:0457acf8690429f1c98ee545cb8573b8\tUR:/nfs/treeoflife-01/resources/<ABS_PATH>\tAS:GCA_922984935.2\tAN:SUPER_1\tSP:Meles meles",
+                    "@SQ\tSN:OV277441.1\tLN:7999920\tM5:0457acf8690429f1c98ee545cb8573b8\tUR:GCA_922984935.2.subset.fasta.gz\tAS:GCA_922984935.2\tAN:SUPER_1\tSP:Meles meles",
                     "@RG\tID:61ddc6c3/15--15\tPL:PACBIO\tDS:READTYPE=CCS;BINDINGKIT=101-789-500;SEQUENCINGKIT=101-826-100;BASECALLERVERSION=5.0.0;FRAMERATEHZ=100.000000;BarcodeFile=/lustre/scratch116/vr/projects/vgp/ref/barcodes/Sequel_16_Barcodes_v3.fasta;BarcodeHash=e418d89cefcbef90f3cb0e6455b7e2a3;BarcodeCount=16;BarcodeMode=Symmetric;BarcodeQuality=Score\tLB:DN615654G-A1\tPU:m64094_200910_173211\tPM:SEQUELII\tBC:CACTCACGTGTGATATT\tCM:S/P4-C2/5.0-8M\tSM:SAMEA7524440",
                     "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t4 -ax map-hifi --cs=short -y -R @RG\\tID:61ddc6c3/15--15\\tPL:PACBIO\\tDS:READTYPE=CCS;BINDINGKIT=101-789-500;SEQUENCINGKIT=101-826-100;BASECALLERVERSION=5.0.0;FRAMERATEHZ=100.000000;BarcodeFile=/lustre/scratch116/vr/projects/vgp/ref/barcodes/Sequel_16_Barcodes_v3.fasta;BarcodeHash=e418d89cefcbef90f3cb0e6455b7e2a3;BarcodeCount=16;BarcodeMode=Symmetric;BarcodeQuality=Score\\tLB:DN615654G-A1\\tPU:m64094_200910_173211\\tPM:SEQUELII\\tBC:CACTCACGTGTGATATT\\tCM:S/P4-C2/5.0-8M\\tSM:SAMEA7524440 -I1G -a GCA_922984935.2.subset.unmasked.mmi -",
                     "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.23.1\tCL:samtools sort -@ 3 -o SAMEA7524440.ERR6939248_other.fastq.gz.0.SAMEA7524440.ERR6939248.bam -T SAMEA7524440.ERR6939248_other.fastq.gz.0.SAMEA7524440.ERR6939248_sort_tmp --write-index -l1 -",
@@ -219,28 +222,27 @@
                 ],
                 "GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.bam": [
                     "@HD\tVN:1.6\tSO:coordinate",
-                    "@SQ\tSN:OV277441.1\tLN:7999920\tM5:0457acf8690429f1c98ee545cb8573b8\tUR:/nfs/treeoflife-01/resources/<ABS_PATH>\tAS:GCA_922984935.2\tAN:SUPER_1\tSP:Meles meles",
-                    "@RG\tID:m64094_200911_174739\tPL:PACBIO\tSM:SAMEA7524440",
-                    "@PG\tID:samtools.extra_header\tPN:samtools\tVN:1.22.1\tCL:samtools collate --output-fmt cram -O -u -T mMelMel3_T4.collate --threads 4 --reference GCA_922984935.2.subset.unmasked.fasta m64094_200911_174739.ccs.bc1022_BAK8B_OA--bc1022_BAK8B_OA.subset.fastq.gz -",
-                    "@PG\tID:samtools.1.extra_header\tPN:samtools\tPP:samtools.extra_header\tVN:1.22.1\tCL:samtools fixmate -m -u --threads 4 - -",
-                    "@PG\tID:samtools.2.extra_header\tPN:samtools\tPP:samtools.1.extra_header\tVN:1.22.1\tCL:samtools sort -u -T mMelMel3_T4.sort --threads 4 -",
-                    "@PG\tID:samtools.3.extra_header\tPN:samtools\tPP:samtools.2.extra_header\tVN:1.22.1\tCL:samtools markdup -T mMelMel3_T4.markdup -f mMelMel3_T4.metrics --threads 4 - mMelMel3_T4.cram",
-                    "@PG\tID:samtools.4.extra_header\tPN:samtools\tPP:samtools.3.extra_header\tVN:1.23.1\tCL:samtools view -H m64094_200911_174739.ccs.bc1022_BAK8B_OA--bc1022_BAK8B_OA.subset.cram",
-                    "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t4 -ax map-hifi --cs=short -y -R @RG\\tID:m64094_200911_174739\\tPL:PACBIO\\tSM:SAMEA7524440 -I1G -a GCA_922984935.2.subset.unmasked.mmi -",
+                    "@SQ\tSN:OV277441.1\tLN:7999920\tM5:0457acf8690429f1c98ee545cb8573b8\tUR:GCA_922984935.2.subset.fasta.gz\tAS:GCA_922984935.2\tAN:SUPER_1\tSP:Meles meles",
+                    "@RG\tID:aaa0cf18/15--15\tPL:PACBIO\tDS:READTYPE=CCS;BINDINGKIT=101-789-500;SEQUENCINGKIT=101-826-100;BASECALLERVERSION=5.0.0;FRAMERATEHZ=100.000000;BarcodeFile=/lustre/scratch116/vr/projects/vgp/ref/barcodes/Sequel_16_Barcodes_v3.fasta;BarcodeHash=e418d89cefcbef90f3cb0e6455b7e2a3;BarcodeCount=16;BarcodeMode=Symmetric;BarcodeQuality=Score\tLB:DN615654G-A1\tPU:m64094_200911_174739\tPM:SEQUELII\tBC:CACTCACGTGTGATATT\tCM:S/P4-C2/5.0-8M\tSM:SAMEA7524440",
+                    "@PG\tID:ccs-4.2.0.extra_header\tPN:ccs\tVN:4.2.0\tDS:Generate circular consensus sequences (ccs) from subreads.\tCL:ccs ccs --chunk 1/64 -j 8 --max-length 50000 ../../m64094_200911_174739.subreads.bam m64094_200911_174739.ccs.bam",
+                    "@PG\tID:lima.extra_header\tVN:1.11.0 (commit v1.11.0)\tCL:lima -j 8 --split-bam-named --same --peek-guess --guess-min-count 1000 --ccs m64094_200911_174739.ccs.bam /lustre/scratch116/vr/projects/vgp/ref/barcodes/Sequel_16_Barcodes_v3.fasta lima/m64094_200911_174739.ccs.bam",
+                    "@PG\tID:samtools.extra_header\tPN:samtools\tVN:1.10\tPP:ccs-4.2.0.extra_header\tCL:samtools merge -@8 -ncp -b m64094_200911_174739.chunks.fofn m64094_200911_174739.ccs.bam",
+                    "@PG\tID:samtools.1.extra_header\tPN:samtools\tPP:samtools.extra_header\tVN:1.23.1\tCL:samtools view -H /lustre/scratch122/tol/data/9/9/f/1/6/d/Meles_meles/genomic_data/mMelMel3/pacbio/m64094_200911_174739.ccs.bc1022_BAK8B_OA--bc1022_BAK8B_OA.bam",
+                    "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t4 -ax map-hifi --cs=short -y -R @RG\\tID:aaa0cf18/15--15\\tPL:PACBIO\\tDS:READTYPE=CCS;BINDINGKIT=101-789-500;SEQUENCINGKIT=101-826-100;BASECALLERVERSION=5.0.0;FRAMERATEHZ=100.000000;BarcodeFile=/lustre/scratch116/vr/projects/vgp/ref/barcodes/Sequel_16_Barcodes_v3.fasta;BarcodeHash=e418d89cefcbef90f3cb0e6455b7e2a3;BarcodeCount=16;BarcodeMode=Symmetric;BarcodeQuality=Score\\tLB:DN615654G-A1\\tPU:m64094_200911_174739\\tPM:SEQUELII\\tBC:CACTCACGTGTGATATT\\tCM:S/P4-C2/5.0-8M\\tSM:SAMEA7524440 -I1G -a GCA_922984935.2.subset.unmasked.mmi -",
                     "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.23.1\tCL:samtools sort -@ 3 -o m64094_200911_174739.ccs.bc1022_BAK8B_OA--bc1022_BAK8B_OA.subset.fastq.gz.0.SAMEA7524440.ERR6939249.bam -T m64094_200911_174739.ccs.bc1022_BAK8B_OA--bc1022_BAK8B_OA.subset.fastq.gz.0.SAMEA7524440.ERR6939249_sort_tmp --write-index -l1 -",
                     "@PG\tID:samtools.1\tPN:samtools\tPP:samtools\tVN:1.23.1\tCL:samtools merge --threads 3 -c -p --reference GCA_922984935.2.subset.unmasked.fa SAMEA7524440.ERR6939249.merge.bam 1/m64094_200911_174739.ccs.bc1022_BAK8B_OA--bc1022_BAK8B_OA.subset.fastq.gz.0.SAMEA7524440.ERR6939249.bam",
                     "@PG\tID:crumble\tPN:crumble\tPP:samtools.1\tVN:0.9.1\tCL:crumble -y pbccs -O bam SAMEA7524440.ERR6939249.merge.bam SAMEA7524440.ERR6939249.merge.crumble.bam",
-                    "@PG\tID:samtools.2\tPN:samtools\tPP:samtools.4.extra_header\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.bam",
+                    "@PG\tID:samtools.2\tPN:samtools\tPP:samtools.1.extra_header\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.bam",
                     "@PG\tID:samtools.3\tPN:samtools\tPP:crumble\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.bam",
                     "@PG\tID:samtools.4\tPN:samtools\tPP:samtools.2\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.bam",
                     "@PG\tID:samtools.5\tPN:samtools\tPP:samtools.3\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.bam"
                 ],
                 "GCA_922984935.2.subset.pacbio.SAMEA7524440.merged_1.minimap2.bam": [
                     "@HD\tVN:1.6\tSO:coordinate",
-                    "@SQ\tSN:OV277441.1\tLN:7999920\tM5:0457acf8690429f1c98ee545cb8573b8\tUR:/nfs/treeoflife-01/resources/<ABS_PATH>\tAS:GCA_922984935.2\tAN:SUPER_1\tSP:Meles meles",
-                    "@RG\tID:m64094_200911_174739\tPL:PACBIO\tSM:SAMEA7524440",
+                    "@SQ\tSN:OV277441.1\tLN:7999920\tM5:0457acf8690429f1c98ee545cb8573b8\tUR:GCA_922984935.2.subset.fasta.gz\tAS:GCA_922984935.2\tAN:SUPER_1\tSP:Meles meles",
+                    "@RG\tID:aaa0cf18/15--15\tPL:PACBIO\tDS:READTYPE=CCS;BINDINGKIT=101-789-500;SEQUENCINGKIT=101-826-100;BASECALLERVERSION=5.0.0;FRAMERATEHZ=100.000000;BarcodeFile=/lustre/scratch116/vr/projects/vgp/ref/barcodes/Sequel_16_Barcodes_v3.fasta;BarcodeHash=e418d89cefcbef90f3cb0e6455b7e2a3;BarcodeCount=16;BarcodeMode=Symmetric;BarcodeQuality=Score\tLB:DN615654G-A1\tPU:m64094_200911_174739\tPM:SEQUELII\tBC:CACTCACGTGTGATATT\tCM:S/P4-C2/5.0-8M\tSM:SAMEA7524440",
                     "@RG\tID:61ddc6c3/15--15\tPL:PACBIO\tDS:READTYPE=CCS;BINDINGKIT=101-789-500;SEQUENCINGKIT=101-826-100;BASECALLERVERSION=5.0.0;FRAMERATEHZ=100.000000;BarcodeFile=/lustre/scratch116/vr/projects/vgp/ref/barcodes/Sequel_16_Barcodes_v3.fasta;BarcodeHash=e418d89cefcbef90f3cb0e6455b7e2a3;BarcodeCount=16;BarcodeMode=Symmetric;BarcodeQuality=Score\tLB:DN615654G-A1\tPU:m64094_200910_173211\tPM:SEQUELII\tBC:CACTCACGTGTGATATT\tCM:S/P4-C2/5.0-8M\tSM:SAMEA7524440",
-                    "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t4 -ax map-hifi --cs=short -y -R @RG\\tID:m64094_200911_174739\\tPL:PACBIO\\tSM:SAMEA7524440 -I1G -a GCA_922984935.2.subset.unmasked.mmi -",
+                    "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t4 -ax map-hifi --cs=short -y -R @RG\\tID:aaa0cf18/15--15\\tPL:PACBIO\\tDS:READTYPE=CCS;BINDINGKIT=101-789-500;SEQUENCINGKIT=101-826-100;BASECALLERVERSION=5.0.0;FRAMERATEHZ=100.000000;BarcodeFile=/lustre/scratch116/vr/projects/vgp/ref/barcodes/Sequel_16_Barcodes_v3.fasta;BarcodeHash=e418d89cefcbef90f3cb0e6455b7e2a3;BarcodeCount=16;BarcodeMode=Symmetric;BarcodeQuality=Score\\tLB:DN615654G-A1\\tPU:m64094_200911_174739\\tPM:SEQUELII\\tBC:CACTCACGTGTGATATT\\tCM:S/P4-C2/5.0-8M\\tSM:SAMEA7524440 -I1G -a GCA_922984935.2.subset.unmasked.mmi -",
                     "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.23.1\tCL:samtools sort -@ 3 -o m64094_200911_174739.ccs.bc1022_BAK8B_OA--bc1022_BAK8B_OA.subset.fastq.gz.0.SAMEA7524440.ERR6939249.bam -T m64094_200911_174739.ccs.bc1022_BAK8B_OA--bc1022_BAK8B_OA.subset.fastq.gz.0.SAMEA7524440.ERR6939249_sort_tmp --write-index -l1 -",
                     "@PG\tID:samtools.1\tPN:samtools\tPP:samtools\tVN:1.23.1\tCL:samtools merge --threads 3 -c -p --reference GCA_922984935.2.subset.unmasked.fa SAMEA7524440.ERR6939249.merge.bam 1/m64094_200911_174739.ccs.bc1022_BAK8B_OA--bc1022_BAK8B_OA.subset.fastq.gz.0.SAMEA7524440.ERR6939249.bam",
                     "@PG\tID:samtools.2\tPN:samtools\tPP:samtools.1\tVN:1.23.1\tCL:samtools merge --threads 3 -c -p SAMEA7524440.merged_1.merge.bam 1/SAMEA7524440.ERR6939249.merge.bam 2/SAMEA7524440.ERR6939248.merge.bam",
@@ -259,6 +261,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.4"
         },
-        "timestamp": "2026-05-29T03:12:18.823237748"
+        "timestamp": "2026-06-03T15:07:54.364990996"
     }
 }
\ No newline at end of file

From 85468305093b049ae134ace4c0985ae374044745 Mon Sep 17 00:00:00 2001
From: Hanh Hoang <134130358+sainsachiko@users.noreply.github.com>
Date: Wed, 3 Jun 2026 23:10:45 +0700
Subject: [PATCH 16/20] Apply suggestions from code review

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Matthieu Muffato <cortexspam-github@yahoo.fr>
Co-authored-by: Hanh Hoang <134130358+sainsachiko@users.noreply.github.com>
---
 .github/workflows/download_pipeline.yml | 2 +-
 assets/schema_input.json                | 4 ++--
 subworkflows/local/input_check.nf       | 2 +-
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml
index 52784804..45884ff9 100644
--- a/.github/workflows/download_pipeline.yml
+++ b/.github/workflows/download_pipeline.yml
@@ -32,7 +32,7 @@ jobs:
         run: |
           echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> "$GITHUB_OUTPUT"
           echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> "$GITHUB_OUTPUT"
-          echo "REPO_BRANCH=${{ github.event_name == 'pull_request' && github.event.pull_request.head.ref || github.event.inputs.testbranch || 'dev' }}" >> "$GITHUB_OUTPUT"
+          echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> "$GITHUB_OUTPUT"
 
   download:
     runs-on: ubuntu-latest
diff --git a/assets/schema_input.json b/assets/schema_input.json
index 70754236..879e4422 100644
--- a/assets/schema_input.json
+++ b/assets/schema_input.json
@@ -50,8 +50,8 @@
                 "type": "string",
                 "format": "file-path",
                 "exists": true,
-                "pattern": "^\\S+\\.(sam|sam.gz)$",
-                "errorMessage": "SAM header file cannot contain spaces and must be in SAM format",
+                "pattern": "^\\S+\\.sam$",
+                "errorMessage": "SAM header file cannot contain spaces and must be an uncompressed SAM file"
                 "meta": ["extra_header"]
             }
         },
diff --git a/subworkflows/local/input_check.nf b/subworkflows/local/input_check.nf
index 4d7134c5..fb8bd8e3 100644
--- a/subworkflows/local/input_check.nf
+++ b/subworkflows/local/input_check.nf
@@ -55,7 +55,7 @@ def create_data_channel ( LinkedHashMap row, datafile, stats ) {
     meta.datatype      = row.datatype
     meta.library       = row.library
     meta.barcode       = row.barcode
-    meta.extra_header  = row.extra_header ? file(row.extra_header, checkIfExists: true) : []
+    meta.extra_header  = row.extra_header ?: []
 
     def platform = (meta.datatype == "hic" || meta.datatype == "illumina") ? "ILLUMINA" :
                 (meta.datatype == "pacbio" || meta.datatype == "pacbio_clr") ? "PACBIO" :

From b3abe170866ed3c2415f949b8c15234f1045b4b2 Mon Sep 17 00:00:00 2001
From: sainsachiko <hthhanh.work@gmail.com>
Date: Wed, 3 Jun 2026 17:17:32 +0100
Subject: [PATCH 17/20] Forgot comma

---
 assets/schema_input.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/assets/schema_input.json b/assets/schema_input.json
index 879e4422..4b2ac6d3 100644
--- a/assets/schema_input.json
+++ b/assets/schema_input.json
@@ -51,7 +51,7 @@
                 "format": "file-path",
                 "exists": true,
                 "pattern": "^\\S+\\.sam$",
-                "errorMessage": "SAM header file cannot contain spaces and must be an uncompressed SAM file"
+                "errorMessage": "SAM header file cannot contain spaces and must be an uncompressed SAM file",
                 "meta": ["extra_header"]
             }
         },

From e4ae1ed7de421728a23f42f7487f55e5874d9050 Mon Sep 17 00:00:00 2001
From: sainsachiko <hthhanh.work@gmail.com>
Date: Thu, 4 Jun 2026 17:58:16 +0100
Subject: [PATCH 18/20] Chaining PG line in header

---
 .../local/samtools/reheader/samtools_replaceheader.nf | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/modules/local/samtools/reheader/samtools_replaceheader.nf b/modules/local/samtools/reheader/samtools_replaceheader.nf
index 93123950..b5435e15 100644
--- a/modules/local/samtools/reheader/samtools_replaceheader.nf
+++ b/modules/local/samtools/reheader/samtools_replaceheader.nf
@@ -14,7 +14,7 @@ process SAMTOOLS_REHEADER {
     output:
     tuple val(meta), path("${prefix}.bam") , optional:true, emit: bam
     tuple val(meta), path("${prefix}.cram"), optional:true, emit: cram
-    tuple val("${task.process}"), val('samtools'), eval("samtools version | sed '1!d;s/.* //'"), topic: versions, emit: versions_samtools
+    tuple val("${task.process}"), val('samtools'), eval("samtools version | sed '1!d;s/.* //'") , topic: versions, emit: versions_samtools
 
     when:
     task.ext.when == null || task.ext.when
@@ -26,6 +26,8 @@ process SAMTOOLS_REHEADER {
     // Suffix all PG IDs from sample extra_header to keep them distinct from native file-header PG IDs.
     // Also rewrite matching PP references so the extra-header PG chain remains intact after suffixing.
     def pg_extra = sample_extra_header ? "awk 'BEGIN { FS = OFS = \"\\t\" } FNR == NR { if (\$1 == \"@PG\") for (i = 1; i <= NF; i++) if (\$i ~ /^ID:/) { ids[substr(\$i, 4)] = 1; break } next } \$1 == \"@PG\" { for (i = 1; i <= NF; i++) { if (\$i ~ /^ID:/) { \$i = \$i \".extra_header\" } else if (\$i ~ /^PP:/) { pp = substr(\$i, 4); if (pp in ids) \$i = \"PP:\" pp \".extra_header\" } } print }' ${sample_extra_header} ${sample_extra_header} || true" : "true"
+    // Last inserted PG ID (after suffix) used to bridge native PG root via PP.
+    def pg_extra_last_id = sample_extra_header ? "awk 'BEGIN { FS = OFS = \"\\t\" } \$1 == \"@PG\" { for (i = 1; i <= NF; i++) if (\$i ~ /^ID:/) { last = substr(\$i, 4) \".extra_header\"; break } } END { if (last != \"\") print last }' ${sample_extra_header}" : "echo ''"
 
     if ("$file" == "${prefix}.${suffix}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
     """
@@ -34,13 +36,14 @@ process SAMTOOLS_REHEADER {
         ${sq_template} ) > temp.header.sam
 
     # custom sort for readability (retain order of insertion but sort groups by tag)
-    # Add PG lines from sample header
+    # Add PG lines from sample header and bridge native PG root to inserted chain
     # Sort order: HD, SQ, RG, extra PG, PG, other
+    bridge_id="\$(${pg_extra_last_id})"
     ( grep ^@HD temp.header.sam || true && \\
     grep ^@SQ temp.header.sam || true && \\
     grep ^@RG temp.header.sam || true && \\
     ${pg_extra} && \\
-    grep ^@PG temp.header.sam || true && \\
+    awk -v bridge_id="\$bridge_id" 'BEGIN { FS = OFS = "\\t" } \$1 == "@PG" { if (!bridged) { has_pp = 0; for (i = 1; i <= NF; i++) if (\$i ~ /^PP:/) { has_pp = 1; break } if (!has_pp && bridge_id != "") \$0 = \$0 OFS "PP:" bridge_id; bridged = 1 } print; next }' temp.header.sam || true && \\
     grep -v -E '^@HD|^@SQ|^@RG|^@PG' temp.header.sam || true; \\
     ) > temp.sorted.header.sam
 
@@ -54,4 +57,4 @@ process SAMTOOLS_REHEADER {
     """
     touch ${prefix}.${suffix}
     """
-}
+}
\ No newline at end of file

From bb4757af35ec2336c85576451debe253cef239c7 Mon Sep 17 00:00:00 2001
From: sainsachiko <hthhanh.work@gmail.com>
Date: Thu, 4 Jun 2026 19:51:52 +0100
Subject: [PATCH 19/20] Reheader SQ in SAMTOOLS_VIEW

---
 conf/modules.config                           |  1 -
 modules.json                                  |  3 +-
 modules/nf-core/samtools/view/main.nf         | 60 +++++++++---
 .../nf-core/samtools/view/samtools-view.diff  | 92 +++++++++++++++++++
 subworkflows/local/align_short.nf             |  2 +-
 subworkflows/local/convert_stats.nf           | 33 +++----
 tests/default.nf.test.snap                    | 85 ++++++++---------
 tests/short_aligner_minimap2.nf.test.snap     | 41 +++------
 tests/uli.nf.test.snap                        |  2 +-
 tests/uli_no_lima.nf.test.snap                |  2 +-
 tests/untrim.nf.test.snap                     | 14 +--
 11 files changed, 213 insertions(+), 122 deletions(-)
 create mode 100644 modules/nf-core/samtools/view/samtools-view.diff

diff --git a/conf/modules.config b/conf/modules.config
index f7f2b817..7c8ee275 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -220,7 +220,6 @@ process {
             // CRAM and index: from SAMTOOLS_CRAM if no header provided, else from SAMTOOLS_INDEX_CRAM
             saveAs: { filename ->
                 if (filename == 'versions.yml'
-                    || (task.process =~ /SAMTOOLS_CRAM/ && params.header && filename.matches('.*\\.(cram|crai)$'))
                     || ((task.process =~ /SAMTOOLS_CRAM/) && filename.endsWith('.bam') )) {
                     return null
                 }
diff --git a/modules.json b/modules.json
index 979208ba..e8eb0fe0 100644
--- a/modules.json
+++ b/modules.json
@@ -130,7 +130,8 @@
                     "samtools/view": {
                         "branch": "master",
                         "git_sha": "2057a0a8dbd67000d08613a556570aa7184a7c89",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/samtools/view/samtools-view.diff"
                     }
                 }
             },
diff --git a/modules/nf-core/samtools/view/main.nf b/modules/nf-core/samtools/view/main.nf
index 724561bf..4031e7fe 100644
--- a/modules/nf-core/samtools/view/main.nf
+++ b/modules/nf-core/samtools/view/main.nf
@@ -12,6 +12,7 @@ process SAMTOOLS_VIEW {
     tuple val(meta2), path(fasta), path(fai)
     tuple val(meta3), path(qname)
     tuple val(meta4), path(bed)
+    tuple val(meta5), path(reheader_header)
     val index_format
 
     output:
@@ -33,6 +34,9 @@ process SAMTOOLS_VIEW {
     def args2 = task.ext.args2 ?: ''
     prefix = task.ext.prefix ?: "${meta.id}"
     def reference = fasta ? "--reference ${fasta}" : ""
+    def args_no_write_index = args.replaceAll(/(^|\\s)--write-index(\\s|$)/, ' ').trim()
+    def should_index = index_format || args.contains('--write-index')
+    def index_opt = index_format == 'bai' ? '-b' : index_format == 'csi' ? '-c' : ''
     file_type = args.contains("--output-fmt sam")
         ? "sam"
         : args.contains("--output-fmt bam")
@@ -57,19 +61,49 @@ process SAMTOOLS_VIEW {
             error("Indexing not compatible with SAM output")
         }
     }
-    """
-    # Note: --threads value represents *additional* CPUs to allocate (total CPUs = 1 + --threads).
-    samtools \\
-        view \\
-        --threads ${task.cpus - 1} \\
-        ${reference} \\
-        ${readnames} \\
-        ${bedfile} \\
-        ${args} \\
-        -o ${output_file} \\
-        ${input} \\
-        ${args2}
-    """
+
+    if (reheader_header) {
+        """
+        # Note: --threads value represents *additional* CPUs to allocate (total CPUs = 1 + --threads).
+        samtools \\
+            view \\
+            --threads ${task.cpus - 1} \\
+            ${reference} \\
+            ${readnames} \\
+            ${bedfile} \\
+            ${args_no_write_index} \\
+            -o ${prefix}.${file_type} \\
+            ${input} \\
+            ${args2}
+
+        # Build a complete header by preserving existing lines and replacing only @SQ from template.
+        ( samtools view --no-PG --header-only ${prefix}.${file_type} | grep -v '^@SQ' && grep '^@SQ' ${reheader_header} ) > temp.reheader.header.sam
+
+        samtools reheader temp.reheader.header.sam ${prefix}.${file_type} > ${prefix}.reheader.${file_type}
+        mv ${prefix}.reheader.${file_type} ${prefix}.${file_type}
+
+        if [[ "${should_index}" == "true" && "${file_type}" != "sam" ]]; then
+            samtools index --threads ${task.cpus - 1} ${index_opt} ${prefix}.${file_type}
+            if [[ -s ${prefix}.unselected.${file_type} ]]; then
+                samtools index --threads ${task.cpus - 1} ${index_opt} ${prefix}.unselected.${file_type}
+            fi
+        fi
+        """
+    } else {
+        """
+        # Note: --threads value represents *additional* CPUs to allocate (total CPUs = 1 + --threads).
+        samtools \\
+            view \\
+            --threads ${task.cpus - 1} \\
+            ${reference} \\
+            ${readnames} \\
+            ${bedfile} \\
+            ${args} \\
+            -o ${output_file} \\
+            ${input} \\
+            ${args2}
+        """
+    }
 
     stub:
     def args = task.ext.args ?: ''
diff --git a/modules/nf-core/samtools/view/samtools-view.diff b/modules/nf-core/samtools/view/samtools-view.diff
new file mode 100644
index 00000000..5b0c9ded
--- /dev/null
+++ b/modules/nf-core/samtools/view/samtools-view.diff
@@ -0,0 +1,92 @@
+Changes in component 'nf-core/samtools/view'
+'modules/nf-core/samtools/view/meta.yml' is unchanged
+'modules/nf-core/samtools/view/environment.yml' is unchanged
+Changes in 'samtools/view/main.nf':
+--- modules/nf-core/samtools/view/main.nf
++++ modules/nf-core/samtools/view/main.nf
+@@ -12,6 +12,7 @@
+     tuple val(meta2), path(fasta), path(fai)
+     tuple val(meta3), path(qname)
+     tuple val(meta4), path(bed)
++    tuple val(meta5), path(reheader_header)
+     val index_format
+ 
+     output:
+@@ -33,6 +34,9 @@
+     def args2 = task.ext.args2 ?: ''
+     prefix = task.ext.prefix ?: "${meta.id}"
+     def reference = fasta ? "--reference ${fasta}" : ""
++    def args_no_write_index = args.replaceAll(/(^|\\s)--write-index(\\s|$)/, ' ').trim()
++    def should_index = index_format || args.contains('--write-index')
++    def index_opt = index_format == 'bai' ? '-b' : index_format == 'csi' ? '-c' : ''
+     file_type = args.contains("--output-fmt sam")
+         ? "sam"
+         : args.contains("--output-fmt bam")
+@@ -57,19 +61,49 @@
+             error("Indexing not compatible with SAM output")
+         }
+     }
+-    """
+-    # Note: --threads value represents *additional* CPUs to allocate (total CPUs = 1 + --threads).
+-    samtools \\
+-        view \\
+-        --threads ${task.cpus - 1} \\
+-        ${reference} \\
+-        ${readnames} \\
+-        ${bedfile} \\
+-        ${args} \\
+-        -o ${output_file} \\
+-        ${input} \\
+-        ${args2}
+-    """
++
++    if (reheader_header) {
++        """
++        # Note: --threads value represents *additional* CPUs to allocate (total CPUs = 1 + --threads).
++        samtools \\
++            view \\
++            --threads ${task.cpus - 1} \\
++            ${reference} \\
++            ${readnames} \\
++            ${bedfile} \\
++            ${args_no_write_index} \\
++            -o ${prefix}.${file_type} \\
++            ${input} \\
++            ${args2}
++
++        # Build a complete header by preserving existing lines and replacing only @SQ from template.
++        ( samtools view --no-PG --header-only ${prefix}.${file_type} | grep -v '^@SQ' && grep '^@SQ' ${reheader_header} ) > temp.reheader.header.sam
++
++        samtools reheader temp.reheader.header.sam ${prefix}.${file_type} > ${prefix}.reheader.${file_type}
++        mv ${prefix}.reheader.${file_type} ${prefix}.${file_type}
++
++        if [[ "${should_index}" == "true" && "${file_type}" != "sam" ]]; then
++            samtools index --threads ${task.cpus - 1} ${index_opt} ${prefix}.${file_type}
++            if [[ -s ${prefix}.unselected.${file_type} ]]; then
++                samtools index --threads ${task.cpus - 1} ${index_opt} ${prefix}.unselected.${file_type}
++            fi
++        fi
++        """
++    } else {
++        """
++        # Note: --threads value represents *additional* CPUs to allocate (total CPUs = 1 + --threads).
++        samtools \\
++            view \\
++            --threads ${task.cpus - 1} \\
++            ${reference} \\
++            ${readnames} \\
++            ${bedfile} \\
++            ${args} \\
++            -o ${output_file} \\
++            ${input} \\
++            ${args2}
++        """
++    }
+ 
+     stub:
+     def args = task.ext.args ?: ''
+
+'modules/nf-core/samtools/view/tests/nextflow.config' is unchanged
+'modules/nf-core/samtools/view/tests/main.nf.test' is unchanged
+'modules/nf-core/samtools/view/tests/main.nf.test.snap' is unchanged
+************************************************************
diff --git a/subworkflows/local/align_short.nf b/subworkflows/local/align_short.nf
index 8f285fa2..c2cf4c3d 100644
--- a/subworkflows/local/align_short.nf
+++ b/subworkflows/local/align_short.nf
@@ -34,7 +34,7 @@ workflow ALIGN_SHORT {
     ch_reads_non_crams = ch_reads.non_cram.map { meta, file -> [ meta, file, [] ] }
 
     fasta_dummy_idx = fasta.map { meta, fasta_file -> [ meta, fasta_file, [] ] }
-    CONVERT_CRAM ( ch_reads_non_crams, fasta_dummy_idx, [[],[]], [[],[]], "" )
+    CONVERT_CRAM ( ch_reads_non_crams, fasta_dummy_idx, [[],[]], [[],[]], [[],[]], "" )
 
     // Add read group information to CRAMs if not already present, and merge with CRAMs that already have RG information
     ch_crams_to_addrg = CONVERT_CRAM.out.cram
diff --git a/subworkflows/local/convert_stats.nf b/subworkflows/local/convert_stats.nf
index dac085d4..21b37335 100644
--- a/subworkflows/local/convert_stats.nf
+++ b/subworkflows/local/convert_stats.nf
@@ -5,9 +5,7 @@
 
 // MODULE: local modules
 include { CHANGE_NAME                                   } from '../../modules/local/change_name'
-include { SAMTOOLS_REHEADER as SAMTOOLS_ADD_PG          } from '../../modules/local/samtools/reheader/samtools_replaceheader'
 include { SAMTOOLS_REHEADER as SAMTOOLS_REHEADER_BAM    } from '../../modules/local/samtools/reheader/samtools_replaceheader'
-include { SAMTOOLS_REHEADER as SAMTOOLS_REHEADER_CRAM   } from '../../modules/local/samtools/reheader/samtools_replaceheader'
 
 // MODULE: nf-core modules
 include { BLOBTK_DEPTH                              } from '../../modules/nf-core/blobtk/depth/main'
@@ -15,7 +13,6 @@ include { CRUMBLE                                   } from '../../modules/nf-cor
 include { PIGZ_COMPRESS as GZIP_STATS               } from '../../modules/nf-core/pigz/compress/main'
 include { SAMTOOLS_VIEW as SAMTOOLS_CRAM            } from '../../modules/nf-core/samtools/view/main'
 include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_BAM      } from '../../modules/nf-core/samtools/index/main'
-include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_CRAM     } from '../../modules/nf-core/samtools/index/main'
 include { SAMTOOLS_STATS                            } from '../../modules/nf-core/samtools/stats/main'
 include { SAMTOOLS_FLAGSTAT                         } from '../../modules/nf-core/samtools/flagstat/main'
 include { SAMTOOLS_IDXSTATS                         } from '../../modules/nf-core/samtools/idxstats/main'
@@ -57,16 +54,18 @@ workflow CONVERT_STATS {
     // Change name of BAM files to final name for publishing
     CHANGE_NAME ( ch_bams_for_renaming, fasta )
 
+    header_value = params.header ? header.first() : channel.value([])
     ch_renamed_bams = CHANGE_NAME.out.file
     .branch { meta, bam_file ->
-        extra_header: meta.add_pg
-            return [ meta, bam_file, meta.extra_header ]
-        no_extra_header: true
+        reheader: (params.header || meta.add_pg)
+            return [ meta, bam_file, (meta.add_pg ? meta.extra_header : []) ]
+        passthrough: true
     }
 
-    SAMTOOLS_ADD_PG( ch_renamed_bams.extra_header, [] )
-    ch_bams_add_pg = SAMTOOLS_ADD_PG.out.bam
-    .mix( ch_renamed_bams.no_extra_header )
+    // Reheader only when needed: optional template header and/or sample extra @PG.
+    SAMTOOLS_REHEADER_BAM( ch_renamed_bams.reheader, header_value )
+    ch_bams_reheadered = SAMTOOLS_REHEADER_BAM.out.bam
+    .mix( ch_renamed_bams.passthrough )
     .map { meta, bam_file -> [ meta, bam_file, [] ] }
 
     // (Optionally) convert to CRAM if it's specified in outfmt
@@ -74,18 +73,12 @@ workflow CONVERT_STATS {
     ch_crai = channel.empty()
 
     fasta_dummy_idx = fasta.map { meta, fasta_file -> [ meta, fasta_file, [] ] }
+    cram_reheader_header = params.header ? header_value.map { hdr -> [[], hdr] } : [[],[]]
     if ( "cram" in outfmt_options ) {
-        SAMTOOLS_CRAM ( ch_bams_add_pg, fasta_dummy_idx, [[],[]], [[],[]], "" )
+        SAMTOOLS_CRAM ( ch_bams_reheadered, fasta_dummy_idx, [[],[]], [[],[]], cram_reheader_header, "" )
         ch_cram = SAMTOOLS_CRAM.out.cram
         ch_crai = SAMTOOLS_CRAM.out.crai
 
-        if ( params.header ) {
-            SAMTOOLS_REHEADER_CRAM ( SAMTOOLS_CRAM.out.cram.map{ meta, cram -> [ meta, cram, []] }, header.first() )
-            SAMTOOLS_INDEX_CRAM ( SAMTOOLS_REHEADER_CRAM.out.cram )
-            ch_cram = SAMTOOLS_INDEX_CRAM.out.input
-            ch_crai = SAMTOOLS_INDEX_CRAM.out.index
-        }
-
         // Combine CRAM and CRAI into one channel
         ch_for_stats = ch_cram.join ( ch_crai )
     }
@@ -95,8 +88,8 @@ workflow CONVERT_STATS {
     ch_bai = channel.empty()
 
     if ( "bam" in outfmt_options ) {
-        // Re-header && reindex BAM
-        ch_bam = params.header ? SAMTOOLS_REHEADER_BAM ( ch_bams_add_pg, header.first() ).bam : ch_bams_add_pg.map{ meta, bam_file, _empty -> [ meta, bam_file ] }
+        // Reindex BAM already processed by unified reheader step.
+        ch_bam = ch_bams_reheadered.map{ meta, bam_file, _empty -> [ meta, bam_file ] }
         SAMTOOLS_INDEX_BAM ( ch_bam )
 
         // Set the BAM and BAI channels for emission
@@ -110,7 +103,7 @@ workflow CONVERT_STATS {
     }
 
     // Calculate read depth
-    BLOBTK_DEPTH ( ch_bams_add_pg )
+    BLOBTK_DEPTH ( ch_bams_reheadered )
     BGZIP_BEDGRAPH ( BLOBTK_DEPTH.out.bed )
 
     // Calculate statistics
diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap
index da6fbc45..d98898ae 100644
--- a/tests/default.nf.test.snap
+++ b/tests/default.nf.test.snap
@@ -1,7 +1,7 @@
 {
     "-profile test": {
         "content": [
-            183,
+            171,
             {
                 "BGZIP_BEDGRAPH": {
                     "samtools": "1.23.1"
@@ -73,9 +73,6 @@
                 "SAMTOOLS_ADDREPLACERG": {
                     "samtools": "1.23.1"
                 },
-                "SAMTOOLS_ADD_PG": {
-                    "samtools": "1.23.1"
-                },
                 "SAMTOOLS_CRAM": {
                     "samtools": "1.23.1"
                 },
@@ -94,16 +91,13 @@
                 "SAMTOOLS_INDEX": {
                     "samtools": "1.23.1"
                 },
-                "SAMTOOLS_INDEX_CRAM": {
-                    "samtools": "1.23.1"
-                },
                 "SAMTOOLS_MERGE": {
                     "samtools": "1.23.1"
                 },
                 "SAMTOOLS_MERGEDUP": {
                     "samtools": "1.23.1"
                 },
-                "SAMTOOLS_REHEADER_CRAM": {
+                "SAMTOOLS_REHEADER_BAM": {
                     "samtools": "1.23.1"
                 },
                 "SAMTOOLS_SPLITHEADER": {
@@ -410,19 +404,16 @@
                     "@PG\tID:samtools.3.extra_header\tPN:samtools\tPP:scramble.extra_header\tVN:1.15\tCL:/usr/local/bin/samtools view -h /lustre/scratch124/tol/projects/darwin/data/mammals/Meles_meles/genomic_data/mMelMel3/hic-arima2/35528_2#1.cram",
                     "@PG\tID:samtools.4.extra_header\tPN:samtools\tPP:samtools.3.extra_header\tVN:1.20\tCL:/usr/local/bin/samtools view --cram 35528_2#1.subset.sam",
                     "@PG\tID:samtools.5.extra_header\tPN:samtools\tPP:samtools.4.extra_header\tVN:1.23.1\tCL:samtools view -H 35528_2_1.subset.cram",
-                    "@PG\tID:bwa-mem2\tPN:bwa-mem2\tVN:2.2.1\tCL:bwa-mem2 mem -5SPCp -t 4 ./bwamem2/GCA_922984935.2.subset.unmasked.fa -C -H @RG\\tID:35528_2#1\\tDT:2020-11-17T00:00:00+0000\\tPU:201117_A00948_0206_AHGML2DSXY_2#1\\tLB:33637906\\tPG:SCS\\tSM:SAMEA5962964\\tCN:SC\\tPL:ILLUMINA\\tDS:ERP116890: Sequencing and assembly of genomes from British species for the Darwin Tree of Life Project. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/  -",
+                    "@PG\tID:bwa-mem2\tPN:bwa-mem2\tVN:2.2.1\tCL:bwa-mem2 mem -5SPCp -t 4 ./bwamem2/GCA_922984935.2.subset.unmasked.fa -C -H @RG\\tID:35528_2#1\\tDT:2020-11-17T00:00:00+0000\\tPU:201117_A00948_0206_AHGML2DSXY_2#1\\tLB:33637906\\tPG:SCS\\tSM:SAMEA5962964\\tCN:SC\\tPL:ILLUMINA\\tDS:ERP116890: Sequencing and assembly of genomes from British species for the Darwin Tree of Life Project. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/  -\tPP:samtools.5.extra_header",
                     "@PG\tID:samtools\tPN:samtools\tPP:bwa-mem2\tVN:1.22.1\tCL:samtools fixmate -mpu - -",
                     "@PG\tID:samtools.1\tPN:samtools\tPP:samtools\tVN:1.22.1\tCL:samtools view -h",
                     "@PG\tID:samtools.2\tPN:samtools\tPP:samtools.1\tVN:1.22.1\tCL:samtools sort --write-index -l1 -@4 -T 35528_2_1.subset.cram.0.SAMEA7524440.ERR6688402_tmp -o 35528_2_1.subset.cram.0.SAMEA7524440.ERR6688402.bam -",
                     "@PG\tID:samtools.3\tPN:samtools\tPP:samtools.2\tVN:1.23.1\tCL:samtools merge --threads 3 -c -p --reference GCA_922984935.2.subset.unmasked.fa - 1/35528_2_1.subset.cram.0.SAMEA7524440.ERR6688402.bam 2/35528_2_1.subset.cram.1.SAMEA7524440.ERR6688402.bam",
                     "@PG\tID:samtools.4\tPN:samtools\tPP:samtools.3\tVN:1.23.1\tCL:samtools markdup -T SAMEA7524440.ERR6688402 -f SAMEA7524440.ERR6688402.metrics --threads 4 --reference GCA_922984935.2.subset.unmasked.fa - SAMEA7524440.ERR6688402.bam",
                     "@PG\tID:crumble\tPN:crumble\tPP:samtools.4\tVN:0.9.1\tCL:crumble -O bam SAMEA7524440.ERR6688402.bam SAMEA7524440.ERR6688402.crumble.bam",
-                    "@PG\tID:samtools.5\tPN:samtools\tPP:samtools.5.extra_header\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.bwamem2.bam",
-                    "@PG\tID:samtools.6\tPN:samtools\tPP:crumble\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.bwamem2.bam",
-                    "@PG\tID:samtools.7\tPN:samtools\tPP:samtools.5\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1,lossy_names=1 --write-index -o GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.bwamem2.cram GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.bwamem2.bam",
-                    "@PG\tID:samtools.8\tPN:samtools\tPP:samtools.6\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1,lossy_names=1 --write-index -o GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.bwamem2.cram GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.bwamem2.bam",
-                    "@PG\tID:samtools.9\tPN:samtools\tPP:samtools.7\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.bwamem2.cram",
-                    "@PG\tID:samtools.10\tPN:samtools\tPP:samtools.8\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.bwamem2.cram"
+                    "@PG\tID:samtools.5\tPN:samtools\tPP:crumble\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.bwamem2.bam",
+                    "@PG\tID:samtools.6\tPN:samtools\tPP:samtools.5\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1,lossy_names=1 --write-index -o GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.bwamem2.cram GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.bwamem2.bam",
+                    "@PG\tID:samtools.7\tPN:samtools\tPP:samtools.6\tVN:1.23.1\tCL:samtools reheader temp.reheader.header.sam GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.bwamem2.cram"
                 ],
                 "GCA_922984935.2.subset.illumina.SAMEA7524438.ERR6688599.bwamem2.cram": [
                     "@HD\tVN:1.6\tSO:coordinate",
@@ -435,8 +426,9 @@
                     "@PG\tID:samtools.3\tPN:samtools\tPP:samtools.2\tVN:1.23.1\tCL:samtools merge --threads 3 -c -p --reference GCA_922984935.2.subset.unmasked.fa - 1/31231_3_1.subset.cram.0.SAMEA7524438.ERR6688599.bam 2/31231_3_1.subset.cram.1.SAMEA7524438.ERR6688599.bam",
                     "@PG\tID:samtools.4\tPN:samtools\tPP:samtools.3\tVN:1.23.1\tCL:samtools markdup -T SAMEA7524438.ERR6688599 -f SAMEA7524438.ERR6688599.metrics --threads 4 --reference GCA_922984935.2.subset.unmasked.fa - SAMEA7524438.ERR6688599.bam",
                     "@PG\tID:crumble\tPN:crumble\tPP:samtools.4\tVN:0.9.1\tCL:crumble -O bam SAMEA7524438.ERR6688599.bam SAMEA7524438.ERR6688599.crumble.bam",
-                    "@PG\tID:samtools.5\tPN:samtools\tPP:crumble\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1,lossy_names=1 --write-index -o GCA_922984935.2.subset.illumina.SAMEA7524438.ERR6688599.bwamem2.cram GCA_922984935.2.subset.illumina.SAMEA7524438.ERR6688599.bwamem2.bam",
-                    "@PG\tID:samtools.6\tPN:samtools\tPP:samtools.5\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.illumina.SAMEA7524438.ERR6688599.bwamem2.cram"
+                    "@PG\tID:samtools.5\tPN:samtools\tPP:crumble\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.illumina.SAMEA7524438.ERR6688599.bwamem2.bam",
+                    "@PG\tID:samtools.6\tPN:samtools\tPP:samtools.5\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1,lossy_names=1 --write-index -o GCA_922984935.2.subset.illumina.SAMEA7524438.ERR6688599.bwamem2.cram GCA_922984935.2.subset.illumina.SAMEA7524438.ERR6688599.bwamem2.bam",
+                    "@PG\tID:samtools.7\tPN:samtools\tPP:samtools.6\tVN:1.23.1\tCL:samtools reheader temp.reheader.header.sam GCA_922984935.2.subset.illumina.SAMEA7524438.ERR6688599.bwamem2.cram"
                 ],
                 "GCA_922984935.2.subset.illumina.SAMEA7524439.ERR6688600.bwamem2.cram": [
                     "@HD\tVN:1.6\tSO:coordinate",
@@ -449,8 +441,9 @@
                     "@PG\tID:samtools.3\tPN:samtools\tPP:samtools.2\tVN:1.23.1\tCL:samtools merge --threads 3 -c -p --reference GCA_922984935.2.subset.unmasked.fa - 1/SAMEA7524439.ERR6688600_addRG.cram.0.SAMEA7524439.ERR6688600.bam 2/SAMEA7524439.ERR6688600_addRG.cram.1.SAMEA7524439.ERR6688600.bam",
                     "@PG\tID:samtools.4\tPN:samtools\tPP:samtools.3\tVN:1.23.1\tCL:samtools markdup -T SAMEA7524439.ERR6688600 -f SAMEA7524439.ERR6688600.metrics --threads 4 --reference GCA_922984935.2.subset.unmasked.fa - SAMEA7524439.ERR6688600.bam",
                     "@PG\tID:crumble\tPN:crumble\tPP:samtools.4\tVN:0.9.1\tCL:crumble -O bam SAMEA7524439.ERR6688600.bam SAMEA7524439.ERR6688600.crumble.bam",
-                    "@PG\tID:samtools.5\tPN:samtools\tPP:crumble\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1,lossy_names=1 --write-index -o GCA_922984935.2.subset.illumina.SAMEA7524439.ERR6688600.bwamem2.cram GCA_922984935.2.subset.illumina.SAMEA7524439.ERR6688600.bwamem2.bam",
-                    "@PG\tID:samtools.6\tPN:samtools\tPP:samtools.5\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.illumina.SAMEA7524439.ERR6688600.bwamem2.cram"
+                    "@PG\tID:samtools.5\tPN:samtools\tPP:crumble\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.illumina.SAMEA7524439.ERR6688600.bwamem2.bam",
+                    "@PG\tID:samtools.6\tPN:samtools\tPP:samtools.5\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1,lossy_names=1 --write-index -o GCA_922984935.2.subset.illumina.SAMEA7524439.ERR6688600.bwamem2.cram GCA_922984935.2.subset.illumina.SAMEA7524439.ERR6688600.bwamem2.bam",
+                    "@PG\tID:samtools.7\tPN:samtools\tPP:samtools.6\tVN:1.23.1\tCL:samtools reheader temp.reheader.header.sam GCA_922984935.2.subset.illumina.SAMEA7524439.ERR6688600.bwamem2.cram"
                 ],
                 "GCA_922984935.2.subset.ont.SAMEA7524440.PAE35587.minimap2.cram": [
                     "@HD\tVN:1.6\tSO:coordinate",
@@ -459,8 +452,9 @@
                     "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t4 -ax map-ont -y -R @RG\\tID:PAE35587_pass_1f1f0707_115\\tPL:ONT\\tSM:SAMEA7524440 -I1G -a GCA_922984935.2.subset.unmasked.mmi -",
                     "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.23.1\tCL:samtools sort -@ 3 -o PAE35587_pass_1f1f0707_115.subset.fastq.gz.0.SAMEA7524440.PAE35587.bam -T PAE35587_pass_1f1f0707_115.subset.fastq.gz.0.SAMEA7524440.PAE35587_sort_tmp --write-index -l1 -",
                     "@PG\tID:samtools.1\tPN:samtools\tPP:samtools\tVN:1.23.1\tCL:samtools merge --threads 3 -c -p --reference GCA_922984935.2.subset.unmasked.fa SAMEA7524440.PAE35587.merge.bam 1/PAE35587_pass_1f1f0707_115.subset.fastq.gz.0.SAMEA7524440.PAE35587.bam",
-                    "@PG\tID:samtools.2\tPN:samtools\tPP:samtools.1\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1 --write-index -o GCA_922984935.2.subset.ont.SAMEA7524440.PAE35587.minimap2.cram GCA_922984935.2.subset.ont.SAMEA7524440.PAE35587.minimap2.bam",
-                    "@PG\tID:samtools.3\tPN:samtools\tPP:samtools.2\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.ont.SAMEA7524440.PAE35587.minimap2.cram"
+                    "@PG\tID:samtools.2\tPN:samtools\tPP:samtools.1\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.ont.SAMEA7524440.PAE35587.minimap2.bam",
+                    "@PG\tID:samtools.3\tPN:samtools\tPP:samtools.2\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1 --write-index -o GCA_922984935.2.subset.ont.SAMEA7524440.PAE35587.minimap2.cram GCA_922984935.2.subset.ont.SAMEA7524440.PAE35587.minimap2.bam",
+                    "@PG\tID:samtools.4\tPN:samtools\tPP:samtools.3\tVN:1.23.1\tCL:samtools reheader temp.reheader.header.sam GCA_922984935.2.subset.ont.SAMEA7524440.PAE35587.minimap2.cram"
                 ],
                 "GCA_922984935.2.subset.ont.SAMEA7524440.PAE35587_test.minimap2.cram": [
                     "@HD\tVN:1.6\tSO:coordinate",
@@ -469,19 +463,21 @@
                     "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t4 -ax map-ont -y -R @RG\\tID:PAE35587_pass_1f1f0707_115\\tPL:ONT\\tSM:mMelMel3 -I1G -a GCA_922984935.2.subset.unmasked.mmi -",
                     "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.23.1\tCL:samtools sort -@ 3 -o SAMEA7524440.PAE35587_test_other.fastq.gz.0.SAMEA7524440.PAE35587_test.bam -T SAMEA7524440.PAE35587_test_other.fastq.gz.0.SAMEA7524440.PAE35587_test_sort_tmp --write-index -l1 -",
                     "@PG\tID:samtools.1\tPN:samtools\tPP:samtools\tVN:1.23.1\tCL:samtools merge --threads 3 -c -p --reference GCA_922984935.2.subset.unmasked.fa SAMEA7524440.PAE35587_test.merge.bam 1/SAMEA7524440.PAE35587_test_other.fastq.gz.0.SAMEA7524440.PAE35587_test.bam",
-                    "@PG\tID:samtools.2\tPN:samtools\tPP:samtools.1\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1 --write-index -o GCA_922984935.2.subset.ont.SAMEA7524440.PAE35587_test.minimap2.cram GCA_922984935.2.subset.ont.SAMEA7524440.PAE35587_test.minimap2.bam",
-                    "@PG\tID:samtools.3\tPN:samtools\tPP:samtools.2\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.ont.SAMEA7524440.PAE35587_test.minimap2.cram"
+                    "@PG\tID:samtools.2\tPN:samtools\tPP:samtools.1\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.ont.SAMEA7524440.PAE35587_test.minimap2.bam",
+                    "@PG\tID:samtools.3\tPN:samtools\tPP:samtools.2\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1 --write-index -o GCA_922984935.2.subset.ont.SAMEA7524440.PAE35587_test.minimap2.cram GCA_922984935.2.subset.ont.SAMEA7524440.PAE35587_test.minimap2.bam",
+                    "@PG\tID:samtools.4\tPN:samtools\tPP:samtools.3\tVN:1.23.1\tCL:samtools reheader temp.reheader.header.sam GCA_922984935.2.subset.ont.SAMEA7524440.PAE35587_test.minimap2.cram"
                 ],
                 "GCA_922984935.2.subset.ont.SAMEA7524440.merged_1.minimap2.cram": [
                     "@HD\tVN:1.6\tSO:coordinate",
                     "@SQ\tSN:OV277441.1\tLN:7999920\tM5:0457acf8690429f1c98ee545cb8573b8\tUR:GCA_922984935.2.subset.fasta.gz\tAS:GCA_922984935.2\tAN:SUPER_1\tSP:Meles meles",
-                    "@RG\tID:PAE35587_pass_1f1f0707_115\tPL:ONT\tSM:SAMEA7524440",
-                    "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t4 -ax map-ont -y -R @RG\\tID:PAE35587_pass_1f1f0707_115\\tPL:ONT\\tSM:SAMEA7524440 -I1G -a GCA_922984935.2.subset.unmasked.mmi -",
-                    "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.23.1\tCL:samtools sort -@ 3 -o PAE35587_pass_1f1f0707_115.subset.fastq.gz.0.SAMEA7524440.PAE35587.bam -T PAE35587_pass_1f1f0707_115.subset.fastq.gz.0.SAMEA7524440.PAE35587_sort_tmp --write-index -l1 -",
-                    "@PG\tID:samtools.1\tPN:samtools\tPP:samtools\tVN:1.23.1\tCL:samtools merge --threads 3 -c -p --reference GCA_922984935.2.subset.unmasked.fa SAMEA7524440.PAE35587.merge.bam 1/PAE35587_pass_1f1f0707_115.subset.fastq.gz.0.SAMEA7524440.PAE35587.bam",
-                    "@PG\tID:samtools.2\tPN:samtools\tPP:samtools.1\tVN:1.23.1\tCL:samtools merge --threads 3 -c -p SAMEA7524440.merged_1.merge.bam 1/SAMEA7524440.PAE35587.merge.bam 2/SAMEA7524440.PAE35587_test.merge.bam",
-                    "@PG\tID:samtools.3\tPN:samtools\tPP:samtools.2\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1 --write-index -o GCA_922984935.2.subset.ont.SAMEA7524440.merged_1.minimap2.cram GCA_922984935.2.subset.ont.SAMEA7524440.merged_1.minimap2.bam",
-                    "@PG\tID:samtools.4\tPN:samtools\tPP:samtools.3\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.ont.SAMEA7524440.merged_1.minimap2.cram"
+                    "@RG\tID:PAE35587_pass_1f1f0707_115\tPL:ONT\tSM:mMelMel3",
+                    "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t4 -ax map-ont -y -R @RG\\tID:PAE35587_pass_1f1f0707_115\\tPL:ONT\\tSM:mMelMel3 -I1G -a GCA_922984935.2.subset.unmasked.mmi -",
+                    "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.23.1\tCL:samtools sort -@ 3 -o SAMEA7524440.PAE35587_test_other.fastq.gz.0.SAMEA7524440.PAE35587_test.bam -T SAMEA7524440.PAE35587_test_other.fastq.gz.0.SAMEA7524440.PAE35587_test_sort_tmp --write-index -l1 -",
+                    "@PG\tID:samtools.1\tPN:samtools\tPP:samtools\tVN:1.23.1\tCL:samtools merge --threads 3 -c -p --reference GCA_922984935.2.subset.unmasked.fa SAMEA7524440.PAE35587_test.merge.bam 1/SAMEA7524440.PAE35587_test_other.fastq.gz.0.SAMEA7524440.PAE35587_test.bam",
+                    "@PG\tID:samtools.2\tPN:samtools\tPP:samtools.1\tVN:1.23.1\tCL:samtools merge --threads 3 -c -p SAMEA7524440.merged_1.merge.bam 1/SAMEA7524440.PAE35587_test.merge.bam 2/SAMEA7524440.PAE35587.merge.bam",
+                    "@PG\tID:samtools.3\tPN:samtools\tPP:samtools.2\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.ont.SAMEA7524440.merged_1.minimap2.bam",
+                    "@PG\tID:samtools.4\tPN:samtools\tPP:samtools.3\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1 --write-index -o GCA_922984935.2.subset.ont.SAMEA7524440.merged_1.minimap2.cram GCA_922984935.2.subset.ont.SAMEA7524440.merged_1.minimap2.bam",
+                    "@PG\tID:samtools.5\tPN:samtools\tPP:samtools.4\tVN:1.23.1\tCL:samtools reheader temp.reheader.header.sam GCA_922984935.2.subset.ont.SAMEA7524440.merged_1.minimap2.cram"
                 ],
                 "GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939248.minimap2.cram": [
                     "@HD\tVN:1.6\tSO:coordinate",
@@ -492,16 +488,13 @@
                     "@PG\tID:samtools.extra_header\tPN:samtools\tVN:1.10\tPP:ccs-4.2.0.extra_header\tCL:samtools merge -@8 -ncp -b m64094_200910_173211.chunks.fofn m64094_200910_173211.ccs.bam",
                     "@PG\tID:samtools.1.extra_header\tPN:samtools\tPP:samtools.extra_header\tVN:1.19.2\tCL:samtools view -b -h -N /nfs/users/nfs_m/mm49/READS -o /nfs/users/nfs_m/mm49/x.bam m64094_200910_173211.ccs.bc1022_BAK8B_OA--bc1022_BAK8B_OA.bam",
                     "@PG\tID:samtools.2.extra_header\tPN:samtools\tPP:samtools.1.extra_header\tVN:1.23.1\tCL:samtools view -H m64094_200910_173211.ccs.bc1022_BAK8B_OA--bc1022_BAK8B_OA.subset.bam",
-                    "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t4 -ax map-hifi --cs=short -y -R @RG\\tID:61ddc6c3/15--15\\tPL:PACBIO\\tDS:READTYPE=CCS;BINDINGKIT=101-789-500;SEQUENCINGKIT=101-826-100;BASECALLERVERSION=5.0.0;FRAMERATEHZ=100.000000;BarcodeFile=/lustre/scratch116/vr/projects/vgp/ref/barcodes/Sequel_16_Barcodes_v3.fasta;BarcodeHash=e418d89cefcbef90f3cb0e6455b7e2a3;BarcodeCount=16;BarcodeMode=Symmetric;BarcodeQuality=Score\\tLB:DN615654G-A1\\tPU:m64094_200910_173211\\tPM:SEQUELII\\tBC:CACTCACGTGTGATATT\\tCM:S/P4-C2/5.0-8M\\tSM:SAMEA7524440 -I1G -a GCA_922984935.2.subset.unmasked.mmi -",
+                    "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t4 -ax map-hifi --cs=short -y -R @RG\\tID:61ddc6c3/15--15\\tPL:PACBIO\\tDS:READTYPE=CCS;BINDINGKIT=101-789-500;SEQUENCINGKIT=101-826-100;BASECALLERVERSION=5.0.0;FRAMERATEHZ=100.000000;BarcodeFile=/lustre/scratch116/vr/projects/vgp/ref/barcodes/Sequel_16_Barcodes_v3.fasta;BarcodeHash=e418d89cefcbef90f3cb0e6455b7e2a3;BarcodeCount=16;BarcodeMode=Symmetric;BarcodeQuality=Score\\tLB:DN615654G-A1\\tPU:m64094_200910_173211\\tPM:SEQUELII\\tBC:CACTCACGTGTGATATT\\tCM:S/P4-C2/5.0-8M\\tSM:SAMEA7524440 -I1G -a GCA_922984935.2.subset.unmasked.mmi -\tPP:samtools.2.extra_header",
                     "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.23.1\tCL:samtools sort -@ 3 -o pacbio.SAMEA7524440.ERR6939248.hifitrimmer.fastq.gz.0.SAMEA7524440.ERR6939248.bam -T pacbio.SAMEA7524440.ERR6939248.hifitrimmer.fastq.gz.0.SAMEA7524440.ERR6939248_sort_tmp --write-index -l1 -",
                     "@PG\tID:samtools.1\tPN:samtools\tPP:samtools\tVN:1.23.1\tCL:samtools merge --threads 3 -c -p --reference GCA_922984935.2.subset.unmasked.fa SAMEA7524440.ERR6939248.merge.bam 1/pacbio.SAMEA7524440.ERR6939248.hifitrimmer.fastq.gz.0.SAMEA7524440.ERR6939248.bam",
                     "@PG\tID:crumble\tPN:crumble\tPP:samtools.1\tVN:0.9.1\tCL:crumble -y pbccs -O bam SAMEA7524440.ERR6939248.merge.bam SAMEA7524440.ERR6939248.merge.crumble.bam",
-                    "@PG\tID:samtools.2\tPN:samtools\tPP:samtools.2.extra_header\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939248.minimap2.bam",
-                    "@PG\tID:samtools.3\tPN:samtools\tPP:crumble\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939248.minimap2.bam",
-                    "@PG\tID:samtools.4\tPN:samtools\tPP:samtools.2\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1 --write-index -o GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939248.minimap2.cram GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939248.minimap2.bam",
-                    "@PG\tID:samtools.5\tPN:samtools\tPP:samtools.3\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1 --write-index -o GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939248.minimap2.cram GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939248.minimap2.bam",
-                    "@PG\tID:samtools.6\tPN:samtools\tPP:samtools.4\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939248.minimap2.cram",
-                    "@PG\tID:samtools.7\tPN:samtools\tPP:samtools.5\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939248.minimap2.cram"
+                    "@PG\tID:samtools.2\tPN:samtools\tPP:crumble\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939248.minimap2.bam",
+                    "@PG\tID:samtools.3\tPN:samtools\tPP:samtools.2\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1 --write-index -o GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939248.minimap2.cram GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939248.minimap2.bam",
+                    "@PG\tID:samtools.4\tPN:samtools\tPP:samtools.3\tVN:1.23.1\tCL:samtools reheader temp.reheader.header.sam GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939248.minimap2.cram"
                 ],
                 "GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.cram": [
                     "@HD\tVN:1.6\tSO:coordinate",
@@ -511,16 +504,13 @@
                     "@PG\tID:lima.extra_header\tVN:1.11.0 (commit v1.11.0)\tCL:lima -j 8 --split-bam-named --same --peek-guess --guess-min-count 1000 --ccs m64094_200911_174739.ccs.bam /lustre/scratch116/vr/projects/vgp/ref/barcodes/Sequel_16_Barcodes_v3.fasta lima/m64094_200911_174739.ccs.bam",
                     "@PG\tID:samtools.extra_header\tPN:samtools\tVN:1.10\tPP:ccs-4.2.0.extra_header\tCL:samtools merge -@8 -ncp -b m64094_200911_174739.chunks.fofn m64094_200911_174739.ccs.bam",
                     "@PG\tID:samtools.1.extra_header\tPN:samtools\tPP:samtools.extra_header\tVN:1.23.1\tCL:samtools view -H /lustre/scratch122/tol/data/9/9/f/1/6/d/Meles_meles/genomic_data/mMelMel3/pacbio/m64094_200911_174739.ccs.bc1022_BAK8B_OA--bc1022_BAK8B_OA.bam",
-                    "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t4 -ax map-hifi --cs=short -y -R @RG\\tID:aaa0cf18/15--15\\tPL:PACBIO\\tDS:READTYPE=CCS;BINDINGKIT=101-789-500;SEQUENCINGKIT=101-826-100;BASECALLERVERSION=5.0.0;FRAMERATEHZ=100.000000;BarcodeFile=/lustre/scratch116/vr/projects/vgp/ref/barcodes/Sequel_16_Barcodes_v3.fasta;BarcodeHash=e418d89cefcbef90f3cb0e6455b7e2a3;BarcodeCount=16;BarcodeMode=Symmetric;BarcodeQuality=Score\\tLB:DN615654G-A1\\tPU:m64094_200911_174739\\tPM:SEQUELII\\tBC:CACTCACGTGTGATATT\\tCM:S/P4-C2/5.0-8M\\tSM:SAMEA7524440 -I1G -a GCA_922984935.2.subset.unmasked.mmi -",
+                    "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t4 -ax map-hifi --cs=short -y -R @RG\\tID:aaa0cf18/15--15\\tPL:PACBIO\\tDS:READTYPE=CCS;BINDINGKIT=101-789-500;SEQUENCINGKIT=101-826-100;BASECALLERVERSION=5.0.0;FRAMERATEHZ=100.000000;BarcodeFile=/lustre/scratch116/vr/projects/vgp/ref/barcodes/Sequel_16_Barcodes_v3.fasta;BarcodeHash=e418d89cefcbef90f3cb0e6455b7e2a3;BarcodeCount=16;BarcodeMode=Symmetric;BarcodeQuality=Score\\tLB:DN615654G-A1\\tPU:m64094_200911_174739\\tPM:SEQUELII\\tBC:CACTCACGTGTGATATT\\tCM:S/P4-C2/5.0-8M\\tSM:SAMEA7524440 -I1G -a GCA_922984935.2.subset.unmasked.mmi -\tPP:samtools.1.extra_header",
                     "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.23.1\tCL:samtools sort -@ 3 -o pacbio.SAMEA7524440.ERR6939249.hifitrimmer.fastq.gz.0.SAMEA7524440.ERR6939249.bam -T pacbio.SAMEA7524440.ERR6939249.hifitrimmer.fastq.gz.0.SAMEA7524440.ERR6939249_sort_tmp --write-index -l1 -",
                     "@PG\tID:samtools.1\tPN:samtools\tPP:samtools\tVN:1.23.1\tCL:samtools merge --threads 3 -c -p --reference GCA_922984935.2.subset.unmasked.fa SAMEA7524440.ERR6939249.merge.bam 1/pacbio.SAMEA7524440.ERR6939249.hifitrimmer.fastq.gz.0.SAMEA7524440.ERR6939249.bam",
                     "@PG\tID:crumble\tPN:crumble\tPP:samtools.1\tVN:0.9.1\tCL:crumble -y pbccs -O bam SAMEA7524440.ERR6939249.merge.bam SAMEA7524440.ERR6939249.merge.crumble.bam",
-                    "@PG\tID:samtools.2\tPN:samtools\tPP:samtools.1.extra_header\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.bam",
-                    "@PG\tID:samtools.3\tPN:samtools\tPP:crumble\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.bam",
-                    "@PG\tID:samtools.4\tPN:samtools\tPP:samtools.2\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1 --write-index -o GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.cram GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.bam",
-                    "@PG\tID:samtools.5\tPN:samtools\tPP:samtools.3\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1 --write-index -o GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.cram GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.bam",
-                    "@PG\tID:samtools.6\tPN:samtools\tPP:samtools.4\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.cram",
-                    "@PG\tID:samtools.7\tPN:samtools\tPP:samtools.5\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.cram"
+                    "@PG\tID:samtools.2\tPN:samtools\tPP:crumble\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.bam",
+                    "@PG\tID:samtools.3\tPN:samtools\tPP:samtools.2\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1 --write-index -o GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.cram GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.bam",
+                    "@PG\tID:samtools.4\tPN:samtools\tPP:samtools.3\tVN:1.23.1\tCL:samtools reheader temp.reheader.header.sam GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.cram"
                 ],
                 "GCA_922984935.2.subset.pacbio.SAMEA7524440.merged_1.minimap2.cram": [
                     "@HD\tVN:1.6\tSO:coordinate",
@@ -532,8 +522,9 @@
                     "@PG\tID:samtools.1\tPN:samtools\tPP:samtools\tVN:1.23.1\tCL:samtools merge --threads 3 -c -p --reference GCA_922984935.2.subset.unmasked.fa SAMEA7524440.ERR6939248.merge.bam 1/pacbio.SAMEA7524440.ERR6939248.hifitrimmer.fastq.gz.0.SAMEA7524440.ERR6939248.bam",
                     "@PG\tID:samtools.2\tPN:samtools\tPP:samtools.1\tVN:1.23.1\tCL:samtools merge --threads 3 -c -p SAMEA7524440.merged_1.merge.bam 1/SAMEA7524440.ERR6939248.merge.bam 2/SAMEA7524440.ERR6939249.merge.bam",
                     "@PG\tID:crumble\tPN:crumble\tPP:samtools.2\tVN:0.9.1\tCL:crumble -y pbccs -O bam SAMEA7524440.merged_1.merge.bam SAMEA7524440.merged_1.merge.crumble.bam",
-                    "@PG\tID:samtools.3\tPN:samtools\tPP:crumble\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1 --write-index -o GCA_922984935.2.subset.pacbio.SAMEA7524440.merged_1.minimap2.cram GCA_922984935.2.subset.pacbio.SAMEA7524440.merged_1.minimap2.bam",
-                    "@PG\tID:samtools.4\tPN:samtools\tPP:samtools.3\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.merged_1.minimap2.cram"
+                    "@PG\tID:samtools.3\tPN:samtools\tPP:crumble\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.merged_1.minimap2.bam",
+                    "@PG\tID:samtools.4\tPN:samtools\tPP:samtools.3\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1 --write-index -o GCA_922984935.2.subset.pacbio.SAMEA7524440.merged_1.minimap2.cram GCA_922984935.2.subset.pacbio.SAMEA7524440.merged_1.minimap2.bam",
+                    "@PG\tID:samtools.5\tPN:samtools\tPP:samtools.4\tVN:1.23.1\tCL:samtools reheader temp.reheader.header.sam GCA_922984935.2.subset.pacbio.SAMEA7524440.merged_1.minimap2.cram"
                 ]
             },
             [
@@ -545,6 +536,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.4"
         },
-        "timestamp": "2026-06-03T16:06:47.981156535"
+        "timestamp": "2026-06-04T18:14:24.285247311"
     }
 }
\ No newline at end of file
diff --git a/tests/short_aligner_minimap2.nf.test.snap b/tests/short_aligner_minimap2.nf.test.snap
index fcf979ae..eb2b93a0 100644
--- a/tests/short_aligner_minimap2.nf.test.snap
+++ b/tests/short_aligner_minimap2.nf.test.snap
@@ -1,7 +1,7 @@
 {
     "-profile test --short_aligner minimap2 --outfmt 'bam,cram'": {
         "content": [
-            81,
+            74,
             {
                 "BGZIP_BEDGRAPH": {
                     "samtools": "1.23.1"
@@ -46,9 +46,6 @@
                 "SAMTOOLS_ADDREPLACERG": {
                     "samtools": "1.23.1"
                 },
-                "SAMTOOLS_ADD_PG": {
-                    "samtools": "1.23.1"
-                },
                 "SAMTOOLS_CRAM": {
                     "samtools": "1.23.1"
                 },
@@ -67,18 +64,12 @@
                 "SAMTOOLS_INDEX_BAM": {
                     "samtools": "1.23.1"
                 },
-                "SAMTOOLS_INDEX_CRAM": {
-                    "samtools": "1.23.1"
-                },
                 "SAMTOOLS_MERGEDUP": {
                     "samtools": "1.23.1"
                 },
                 "SAMTOOLS_REHEADER_BAM": {
                     "samtools": "1.23.1"
                 },
-                "SAMTOOLS_REHEADER_CRAM": {
-                    "samtools": "1.23.1"
-                },
                 "SAMTOOLS_SPLITHEADER": {
                     "samtools": "1.23.1"
                 },
@@ -250,17 +241,14 @@
                     "@PG\tID:samtools.3.extra_header\tPN:samtools\tPP:scramble.extra_header\tVN:1.15\tCL:/usr/local/bin/samtools view -h /lustre/scratch124/tol/projects/darwin/data/mammals/Meles_meles/genomic_data/mMelMel3/hic-arima2/35528_2#1.cram",
                     "@PG\tID:samtools.4.extra_header\tPN:samtools\tPP:samtools.3.extra_header\tVN:1.20\tCL:/usr/local/bin/samtools view --cram 35528_2#1.subset.sam",
                     "@PG\tID:samtools.5.extra_header\tPN:samtools\tPP:samtools.4.extra_header\tVN:1.23.1\tCL:samtools view -H 35528_2_1.subset.cram",
-                    "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t4 -ax sr --cs=short -I1.0G -y -R @RG\\tID:35528_2#1\\tDT:2020-11-17T00:00:00+0000\\tPU:201117_A00948_0206_AHGML2DSXY_2#1\\tLB:33637906\\tPG:SCS\\tSM:SAMEA5962964\\tCN:SC\\tPL:ILLUMINA\\tDS:ERP116890: Sequencing and assembly of genomes from British species for the Darwin Tree of Life Project. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/  GCA_922984935.2.subset.unmasked.mmi -",
+                    "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t4 -ax sr --cs=short -I1.0G -y -R @RG\\tID:35528_2#1\\tDT:2020-11-17T00:00:00+0000\\tPU:201117_A00948_0206_AHGML2DSXY_2#1\\tLB:33637906\\tPG:SCS\\tSM:SAMEA5962964\\tCN:SC\\tPL:ILLUMINA\\tDS:ERP116890: Sequencing and assembly of genomes from British species for the Darwin Tree of Life Project. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/  GCA_922984935.2.subset.unmasked.mmi -\tPP:samtools.5.extra_header",
                     "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.22.1\tCL:samtools fixmate -mpu - -",
                     "@PG\tID:samtools.1\tPN:samtools\tPP:samtools\tVN:1.22.1\tCL:samtools view -h",
                     "@PG\tID:samtools.2\tPN:samtools\tPP:samtools.1\tVN:1.22.1\tCL:samtools sort --write-index -l1 -@4 -T 35528_2_1.subset.cram.0.SAMEA7524440.ERR6688402_tmp -o 35528_2_1.subset.cram.0.SAMEA7524440.ERR6688402.bam -",
                     "@PG\tID:samtools.3\tPN:samtools\tPP:samtools.2\tVN:1.23.1\tCL:samtools merge --threads 3 -c -p --reference GCA_922984935.2.subset.unmasked.fa - 1/35528_2_1.subset.cram.0.SAMEA7524440.ERR6688402.bam 2/35528_2_1.subset.cram.1.SAMEA7524440.ERR6688402.bam",
                     "@PG\tID:samtools.4\tPN:samtools\tPP:samtools.3\tVN:1.23.1\tCL:samtools markdup -T SAMEA7524440.ERR6688402 -f SAMEA7524440.ERR6688402.metrics --threads 4 --reference GCA_922984935.2.subset.unmasked.fa - SAMEA7524440.ERR6688402.bam",
                     "@PG\tID:crumble\tPN:crumble\tPP:samtools.4\tVN:0.9.1\tCL:crumble -O bam SAMEA7524440.ERR6688402.bam SAMEA7524440.ERR6688402.crumble.bam",
-                    "@PG\tID:samtools.5\tPN:samtools\tPP:samtools.5.extra_header\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.minimap2.bam",
-                    "@PG\tID:samtools.6\tPN:samtools\tPP:crumble\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.minimap2.bam",
-                    "@PG\tID:samtools.7\tPN:samtools\tPP:samtools.5\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.minimap2.bam",
-                    "@PG\tID:samtools.8\tPN:samtools\tPP:samtools.6\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.minimap2.bam"
+                    "@PG\tID:samtools.5\tPN:samtools\tPP:crumble\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.minimap2.bam"
                 ],
                 "GCA_922984935.2.subset.illumina.SAMEA7524438.ERR6688599.minimap2.bam": [
                     "@HD\tVN:1.6\tSO:coordinate",
@@ -310,19 +298,16 @@
                     "@PG\tID:samtools.3.extra_header\tPN:samtools\tPP:scramble.extra_header\tVN:1.15\tCL:/usr/local/bin/samtools view -h /lustre/scratch124/tol/projects/darwin/data/mammals/Meles_meles/genomic_data/mMelMel3/hic-arima2/35528_2#1.cram",
                     "@PG\tID:samtools.4.extra_header\tPN:samtools\tPP:samtools.3.extra_header\tVN:1.20\tCL:/usr/local/bin/samtools view --cram 35528_2#1.subset.sam",
                     "@PG\tID:samtools.5.extra_header\tPN:samtools\tPP:samtools.4.extra_header\tVN:1.23.1\tCL:samtools view -H 35528_2_1.subset.cram",
-                    "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t4 -ax sr --cs=short -I1.0G -y -R @RG\\tID:35528_2#1\\tDT:2020-11-17T00:00:00+0000\\tPU:201117_A00948_0206_AHGML2DSXY_2#1\\tLB:33637906\\tPG:SCS\\tSM:SAMEA5962964\\tCN:SC\\tPL:ILLUMINA\\tDS:ERP116890: Sequencing and assembly of genomes from British species for the Darwin Tree of Life Project. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/  GCA_922984935.2.subset.unmasked.mmi -",
+                    "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t4 -ax sr --cs=short -I1.0G -y -R @RG\\tID:35528_2#1\\tDT:2020-11-17T00:00:00+0000\\tPU:201117_A00948_0206_AHGML2DSXY_2#1\\tLB:33637906\\tPG:SCS\\tSM:SAMEA5962964\\tCN:SC\\tPL:ILLUMINA\\tDS:ERP116890: Sequencing and assembly of genomes from British species for the Darwin Tree of Life Project. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/  GCA_922984935.2.subset.unmasked.mmi -\tPP:samtools.5.extra_header",
                     "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.22.1\tCL:samtools fixmate -mpu - -",
                     "@PG\tID:samtools.1\tPN:samtools\tPP:samtools\tVN:1.22.1\tCL:samtools view -h",
                     "@PG\tID:samtools.2\tPN:samtools\tPP:samtools.1\tVN:1.22.1\tCL:samtools sort --write-index -l1 -@4 -T 35528_2_1.subset.cram.0.SAMEA7524440.ERR6688402_tmp -o 35528_2_1.subset.cram.0.SAMEA7524440.ERR6688402.bam -",
                     "@PG\tID:samtools.3\tPN:samtools\tPP:samtools.2\tVN:1.23.1\tCL:samtools merge --threads 3 -c -p --reference GCA_922984935.2.subset.unmasked.fa - 1/35528_2_1.subset.cram.0.SAMEA7524440.ERR6688402.bam 2/35528_2_1.subset.cram.1.SAMEA7524440.ERR6688402.bam",
                     "@PG\tID:samtools.4\tPN:samtools\tPP:samtools.3\tVN:1.23.1\tCL:samtools markdup -T SAMEA7524440.ERR6688402 -f SAMEA7524440.ERR6688402.metrics --threads 4 --reference GCA_922984935.2.subset.unmasked.fa - SAMEA7524440.ERR6688402.bam",
                     "@PG\tID:crumble\tPN:crumble\tPP:samtools.4\tVN:0.9.1\tCL:crumble -O bam SAMEA7524440.ERR6688402.bam SAMEA7524440.ERR6688402.crumble.bam",
-                    "@PG\tID:samtools.5\tPN:samtools\tPP:samtools.5.extra_header\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.minimap2.bam",
-                    "@PG\tID:samtools.6\tPN:samtools\tPP:crumble\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.minimap2.bam",
-                    "@PG\tID:samtools.7\tPN:samtools\tPP:samtools.5\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1,lossy_names=1 --write-index -o GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.minimap2.cram GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.minimap2.bam",
-                    "@PG\tID:samtools.8\tPN:samtools\tPP:samtools.6\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1,lossy_names=1 --write-index -o GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.minimap2.cram GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.minimap2.bam",
-                    "@PG\tID:samtools.9\tPN:samtools\tPP:samtools.7\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.minimap2.cram",
-                    "@PG\tID:samtools.10\tPN:samtools\tPP:samtools.8\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.minimap2.cram"
+                    "@PG\tID:samtools.5\tPN:samtools\tPP:crumble\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.minimap2.bam",
+                    "@PG\tID:samtools.6\tPN:samtools\tPP:samtools.5\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1,lossy_names=1 --write-index -o GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.minimap2.cram GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.minimap2.bam",
+                    "@PG\tID:samtools.7\tPN:samtools\tPP:samtools.6\tVN:1.23.1\tCL:samtools reheader temp.reheader.header.sam GCA_922984935.2.subset.hic.SAMEA7524440.ERR6688402.minimap2.cram"
                 ],
                 "GCA_922984935.2.subset.illumina.SAMEA7524438.ERR6688599.minimap2.cram": [
                     "@HD\tVN:1.6\tSO:coordinate",
@@ -335,8 +320,9 @@
                     "@PG\tID:samtools.3\tPN:samtools\tPP:samtools.2\tVN:1.23.1\tCL:samtools merge --threads 3 -c -p --reference GCA_922984935.2.subset.unmasked.fa - 1/SAMEA7524438.ERR6688599.cram.0.SAMEA7524438.ERR6688599.bam 2/SAMEA7524438.ERR6688599.cram.1.SAMEA7524438.ERR6688599.bam",
                     "@PG\tID:samtools.4\tPN:samtools\tPP:samtools.3\tVN:1.23.1\tCL:samtools markdup -T SAMEA7524438.ERR6688599 -f SAMEA7524438.ERR6688599.metrics --threads 4 --reference GCA_922984935.2.subset.unmasked.fa - SAMEA7524438.ERR6688599.bam",
                     "@PG\tID:crumble\tPN:crumble\tPP:samtools.4\tVN:0.9.1\tCL:crumble -O bam SAMEA7524438.ERR6688599.bam SAMEA7524438.ERR6688599.crumble.bam",
-                    "@PG\tID:samtools.5\tPN:samtools\tPP:crumble\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1,lossy_names=1 --write-index -o GCA_922984935.2.subset.illumina.SAMEA7524438.ERR6688599.minimap2.cram GCA_922984935.2.subset.illumina.SAMEA7524438.ERR6688599.minimap2.bam",
-                    "@PG\tID:samtools.6\tPN:samtools\tPP:samtools.5\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.illumina.SAMEA7524438.ERR6688599.minimap2.cram"
+                    "@PG\tID:samtools.5\tPN:samtools\tPP:crumble\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.illumina.SAMEA7524438.ERR6688599.minimap2.bam",
+                    "@PG\tID:samtools.6\tPN:samtools\tPP:samtools.5\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1,lossy_names=1 --write-index -o GCA_922984935.2.subset.illumina.SAMEA7524438.ERR6688599.minimap2.cram GCA_922984935.2.subset.illumina.SAMEA7524438.ERR6688599.minimap2.bam",
+                    "@PG\tID:samtools.7\tPN:samtools\tPP:samtools.6\tVN:1.23.1\tCL:samtools reheader temp.reheader.header.sam GCA_922984935.2.subset.illumina.SAMEA7524438.ERR6688599.minimap2.cram"
                 ],
                 "GCA_922984935.2.subset.illumina.SAMEA7524439.ERR6688600.minimap2.cram": [
                     "@HD\tVN:1.6\tSO:coordinate",
@@ -349,8 +335,9 @@
                     "@PG\tID:samtools.3\tPN:samtools\tPP:samtools.2\tVN:1.23.1\tCL:samtools merge --threads 3 -c -p --reference GCA_922984935.2.subset.unmasked.fa - 1/SAMEA7524439.ERR6688600_addRG.cram.0.SAMEA7524439.ERR6688600.bam 2/SAMEA7524439.ERR6688600_addRG.cram.1.SAMEA7524439.ERR6688600.bam",
                     "@PG\tID:samtools.4\tPN:samtools\tPP:samtools.3\tVN:1.23.1\tCL:samtools markdup -T SAMEA7524439.ERR6688600 -f SAMEA7524439.ERR6688600.metrics --threads 4 --reference GCA_922984935.2.subset.unmasked.fa - SAMEA7524439.ERR6688600.bam",
                     "@PG\tID:crumble\tPN:crumble\tPP:samtools.4\tVN:0.9.1\tCL:crumble -O bam SAMEA7524439.ERR6688600.bam SAMEA7524439.ERR6688600.crumble.bam",
-                    "@PG\tID:samtools.5\tPN:samtools\tPP:crumble\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1,lossy_names=1 --write-index -o GCA_922984935.2.subset.illumina.SAMEA7524439.ERR6688600.minimap2.cram GCA_922984935.2.subset.illumina.SAMEA7524439.ERR6688600.minimap2.bam",
-                    "@PG\tID:samtools.6\tPN:samtools\tPP:samtools.5\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.illumina.SAMEA7524439.ERR6688600.minimap2.cram"
+                    "@PG\tID:samtools.5\tPN:samtools\tPP:crumble\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.illumina.SAMEA7524439.ERR6688600.minimap2.bam",
+                    "@PG\tID:samtools.6\tPN:samtools\tPP:samtools.5\tVN:1.23.1\tCL:samtools view --threads 3 --reference GCA_922984935.2.subset.unmasked.fa --output-fmt cram,version=3.0,archive,level=8,embed_ref=1,lossy_names=1 --write-index -o GCA_922984935.2.subset.illumina.SAMEA7524439.ERR6688600.minimap2.cram GCA_922984935.2.subset.illumina.SAMEA7524439.ERR6688600.minimap2.bam",
+                    "@PG\tID:samtools.7\tPN:samtools\tPP:samtools.6\tVN:1.23.1\tCL:samtools reheader temp.reheader.header.sam GCA_922984935.2.subset.illumina.SAMEA7524439.ERR6688600.minimap2.cram"
                 ]
             },
             [
@@ -361,6 +348,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.4"
         },
-        "timestamp": "2026-06-03T15:03:31.017178618"
+        "timestamp": "2026-06-04T18:01:23.719076494"
     }
 }
\ No newline at end of file
diff --git a/tests/uli.nf.test.snap b/tests/uli.nf.test.snap
index 67e31b7e..427e9d44 100644
--- a/tests/uli.nf.test.snap
+++ b/tests/uli.nf.test.snap
@@ -209,6 +209,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.4"
         },
-        "timestamp": "2026-06-03T15:10:45.578688714"
+        "timestamp": "2026-06-04T16:11:38.490048351"
     }
 }
\ No newline at end of file
diff --git a/tests/uli_no_lima.nf.test.snap b/tests/uli_no_lima.nf.test.snap
index ae7ad0e0..f76ac480 100644
--- a/tests/uli_no_lima.nf.test.snap
+++ b/tests/uli_no_lima.nf.test.snap
@@ -202,6 +202,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.4"
         },
-        "timestamp": "2026-06-03T15:01:25.398827197"
+        "timestamp": "2026-06-04T16:08:54.193324076"
     }
 }
\ No newline at end of file
diff --git a/tests/untrim.nf.test.snap b/tests/untrim.nf.test.snap
index 359723b2..513558c7 100644
--- a/tests/untrim.nf.test.snap
+++ b/tests/untrim.nf.test.snap
@@ -1,7 +1,7 @@
 {
     "-profile test --pacbio_adapter_fasta false --pacbio_adapter_yaml false --outfmt bam": {
         "content": [
-            70,
+            69,
             {
                 "BGZIP_BEDGRAPH": {
                     "samtools": "1.23.1"
@@ -39,9 +39,6 @@
                 "MINIMAP2_INDEX": {
                     "minimap2": "2.30-r1287"
                 },
-                "SAMTOOLS_ADD_PG": {
-                    "samtools": "1.23.1"
-                },
                 "SAMTOOLS_FAIDX": {
                     "samtools": "1.23.1"
                 },
@@ -228,14 +225,11 @@
                     "@PG\tID:lima.extra_header\tVN:1.11.0 (commit v1.11.0)\tCL:lima -j 8 --split-bam-named --same --peek-guess --guess-min-count 1000 --ccs m64094_200911_174739.ccs.bam /lustre/scratch116/vr/projects/vgp/ref/barcodes/Sequel_16_Barcodes_v3.fasta lima/m64094_200911_174739.ccs.bam",
                     "@PG\tID:samtools.extra_header\tPN:samtools\tVN:1.10\tPP:ccs-4.2.0.extra_header\tCL:samtools merge -@8 -ncp -b m64094_200911_174739.chunks.fofn m64094_200911_174739.ccs.bam",
                     "@PG\tID:samtools.1.extra_header\tPN:samtools\tPP:samtools.extra_header\tVN:1.23.1\tCL:samtools view -H /lustre/scratch122/tol/data/9/9/f/1/6/d/Meles_meles/genomic_data/mMelMel3/pacbio/m64094_200911_174739.ccs.bc1022_BAK8B_OA--bc1022_BAK8B_OA.bam",
-                    "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t4 -ax map-hifi --cs=short -y -R @RG\\tID:aaa0cf18/15--15\\tPL:PACBIO\\tDS:READTYPE=CCS;BINDINGKIT=101-789-500;SEQUENCINGKIT=101-826-100;BASECALLERVERSION=5.0.0;FRAMERATEHZ=100.000000;BarcodeFile=/lustre/scratch116/vr/projects/vgp/ref/barcodes/Sequel_16_Barcodes_v3.fasta;BarcodeHash=e418d89cefcbef90f3cb0e6455b7e2a3;BarcodeCount=16;BarcodeMode=Symmetric;BarcodeQuality=Score\\tLB:DN615654G-A1\\tPU:m64094_200911_174739\\tPM:SEQUELII\\tBC:CACTCACGTGTGATATT\\tCM:S/P4-C2/5.0-8M\\tSM:SAMEA7524440 -I1G -a GCA_922984935.2.subset.unmasked.mmi -",
+                    "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t4 -ax map-hifi --cs=short -y -R @RG\\tID:aaa0cf18/15--15\\tPL:PACBIO\\tDS:READTYPE=CCS;BINDINGKIT=101-789-500;SEQUENCINGKIT=101-826-100;BASECALLERVERSION=5.0.0;FRAMERATEHZ=100.000000;BarcodeFile=/lustre/scratch116/vr/projects/vgp/ref/barcodes/Sequel_16_Barcodes_v3.fasta;BarcodeHash=e418d89cefcbef90f3cb0e6455b7e2a3;BarcodeCount=16;BarcodeMode=Symmetric;BarcodeQuality=Score\\tLB:DN615654G-A1\\tPU:m64094_200911_174739\\tPM:SEQUELII\\tBC:CACTCACGTGTGATATT\\tCM:S/P4-C2/5.0-8M\\tSM:SAMEA7524440 -I1G -a GCA_922984935.2.subset.unmasked.mmi -\tPP:samtools.1.extra_header",
                     "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.23.1\tCL:samtools sort -@ 3 -o m64094_200911_174739.ccs.bc1022_BAK8B_OA--bc1022_BAK8B_OA.subset.fastq.gz.0.SAMEA7524440.ERR6939249.bam -T m64094_200911_174739.ccs.bc1022_BAK8B_OA--bc1022_BAK8B_OA.subset.fastq.gz.0.SAMEA7524440.ERR6939249_sort_tmp --write-index -l1 -",
                     "@PG\tID:samtools.1\tPN:samtools\tPP:samtools\tVN:1.23.1\tCL:samtools merge --threads 3 -c -p --reference GCA_922984935.2.subset.unmasked.fa SAMEA7524440.ERR6939249.merge.bam 1/m64094_200911_174739.ccs.bc1022_BAK8B_OA--bc1022_BAK8B_OA.subset.fastq.gz.0.SAMEA7524440.ERR6939249.bam",
                     "@PG\tID:crumble\tPN:crumble\tPP:samtools.1\tVN:0.9.1\tCL:crumble -y pbccs -O bam SAMEA7524440.ERR6939249.merge.bam SAMEA7524440.ERR6939249.merge.crumble.bam",
-                    "@PG\tID:samtools.2\tPN:samtools\tPP:samtools.1.extra_header\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.bam",
-                    "@PG\tID:samtools.3\tPN:samtools\tPP:crumble\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.bam",
-                    "@PG\tID:samtools.4\tPN:samtools\tPP:samtools.2\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.bam",
-                    "@PG\tID:samtools.5\tPN:samtools\tPP:samtools.3\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.bam"
+                    "@PG\tID:samtools.2\tPN:samtools\tPP:crumble\tVN:1.23.1\tCL:samtools reheader temp.sorted.header.sam input/GCA_922984935.2.subset.pacbio.SAMEA7524440.ERR6939249.minimap2.bam"
                 ],
                 "GCA_922984935.2.subset.pacbio.SAMEA7524440.merged_1.minimap2.bam": [
                     "@HD\tVN:1.6\tSO:coordinate",
@@ -261,6 +255,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.4"
         },
-        "timestamp": "2026-06-03T15:07:54.364990996"
+        "timestamp": "2026-06-04T15:41:59.639942625"
     }
 }
\ No newline at end of file

From 6eb286b2e3a89cba853b4e1c1e6f0f8963ca0a3c Mon Sep 17 00:00:00 2001
From: sainsachiko <hthhanh.work@gmail.com>
Date: Thu, 4 Jun 2026 20:28:27 +0100
Subject: [PATCH 20/20] Fix pre-commit

---
 modules/local/samtools/reheader/samtools_replaceheader.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/local/samtools/reheader/samtools_replaceheader.nf b/modules/local/samtools/reheader/samtools_replaceheader.nf
index b5435e15..ce84f57e 100644
--- a/modules/local/samtools/reheader/samtools_replaceheader.nf
+++ b/modules/local/samtools/reheader/samtools_replaceheader.nf
@@ -57,4 +57,4 @@ process SAMTOOLS_REHEADER {
     """
     touch ${prefix}.${suffix}
     """
-}
\ No newline at end of file
+}