feat(#4): versions.yml + conf/base.config + conf/modules.config

conf/base.config

@@ -0,0 +1,51 @@
+/*
+ * conf/base.config — portable resource defaults, applied to every run
+ *
+ * Processes declare a resource tier via `label 'process_low'` etc. These are
+ * the fallback values used when no profile-specific `withName:` block overrides
+ * them (e.g., on a local workstation or a non-UCR HPC).
+ *
+ * UCR HPCC annotate runs override per-process with `withName:` blocks in
+ * conf/profile_annotate.config. Provisioning (Lmod module loading) is handled
+ * by conf/provision_ucr_hpcc.config via withLabel: 'antismash' etc.
+ *
+ * Tier summary (base portable values):
+ *   process_single  1 cpu   6 GB    4 h
+ *   process_low     2 cpus  12 GB   8 h
+ *   process_medium  8 cpus  32 GB   24 h
+ *   process_high    16 cpus 64 GB   72 h
+ *   process_long    8 cpus  32 GB  120 h   (duration-bound, moderate memory)
+ */
+
+process {
+
+    withLabel:process_single {
+        cpus   = 1
+        memory = '6 GB'
+        time   = '4 h'
+    }
+
+    withLabel:process_low {
+        cpus   = 2
+        memory = '12 GB'
+        time   = '8 h'
+    }
+
+    withLabel:process_medium {
+        cpus   = 8
+        memory = '32 GB'
+        time   = '24 h'
+    }
+
+    withLabel:process_high {
+        cpus   = 16
+        memory = '64 GB'
+        time   = '72 h'
+    }
+
+    withLabel:process_long {
+        cpus   = 8
+        memory = '32 GB'
+        time   = '120 h'
+    }
+}

conf/modules.config

@@ -0,0 +1,40 @@
+/*
+ * conf/modules.config — per-module publishDir and ext.args
+ *
+ * Keeps process definitions in modules/local/ free of pipeline-specific paths.
+ * Every publishDir that references params.target or other pipeline-level
+ * directories belongs here rather than in the module file.
+ *
+ * ext.args can be used to pass extra CLI flags to tools without editing modules.
+ */
+
+process {
+
+    withName: 'ASM_STATS' {
+        // storeDir handles persistence; no publishDir needed.
+    }
+
+    withName: 'ANTISMASH_RUN' {
+        publishDir = [
+            path:      { params.target },
+            mode:      'copy',
+            overwrite: true
+        ]
+    }
+
+    withName: 'INTERPROSCAN_RUN' {
+        publishDir = [
+            path:      { params.target },
+            mode:      'copy',
+            overwrite: true
+        ]
+    }
+
+    withName: 'SIGNALP_RUN' {
+        publishDir = [
+            path:      { params.target },
+            mode:      'copy',
+            overwrite: true
+        ]
+    }
+}

funannotate.nf

@@ -1796,6 +1796,8 @@ workflow {
     //   postpredict — meta only        no genome filter (annotate/update paths)
     INPUT_CHECK()
     def jobs = INPUT_CHECK.out.genomes
+
+    def ch_versions = Channel.empty()
     if (params.debug.toBoolean()) {
         jobs.view { meta, gz -> "[CHANNEL] Submitting: out=${meta.id}, asmid=${meta.asmid}, transl_table=${meta.transl_table}, gz=${gz}" }
     }
@@ -1875,6 +1877,7 @@ workflow {
                     file(params.samples),
                     file(params.genome_dir)
                 )
+                ch_versions = ch_versions.mix(ASM_STATS.out.versions)
             } else {
                 log.info "Assembly statistics already exist: ${asm_stats_gz}"
             }
@@ -2178,7 +2181,8 @@ workflow {
                 asDir.isDirectory() && asDir.list()?.any { it.endsWith('.json') || it.endsWith('.json.gz') }
             }
             ANTISMASH_RUN(as_todo)
-            def as_completed = ANTISMASH_RUN.out
+            ch_versions = ch_versions.mix(ANTISMASH_RUN.out.versions)
+            def as_completed = ANTISMASH_RUN.out.results
                 .map { meta, _files -> meta }
             annotate_ready_ch = as_completed.mix(as_done)
         }
@@ -2191,7 +2195,8 @@ workflow {
                 file("${params.target}/${meta.id}/annotate_misc/iprscan.xml").exists()
             }
             INTERPROSCAN_RUN(ipr_todo)
-            def ipr_completed = INTERPROSCAN_RUN.out
+            ch_versions = ch_versions.mix(INTERPROSCAN_RUN.out.versions)
+            def ipr_completed = INTERPROSCAN_RUN.out.results
                 .map { meta, _xml -> meta }
             annotate_ready_ch = ipr_completed.mix(ipr_done)
         }
@@ -2204,7 +2209,8 @@ workflow {
                 file("${params.target}/${meta.id}/annotate_misc/signalp.results.txt").exists()
             }
             SIGNALP_RUN(sp_todo)
-            def sp_completed = SIGNALP_RUN.out
+            ch_versions = ch_versions.mix(SIGNALP_RUN.out.versions)
+            def sp_completed = SIGNALP_RUN.out.results
                 .map { meta, _txt -> meta }
             annotate_ready_ch = sp_completed.mix(sp_done)
         }
@@ -2251,5 +2257,15 @@ workflow {
         }
         } // end if (!params.stop_after_sra_fetch || !params.run_sra_fetch)
     }
+
+    // Collect software versions from all processes that emit versions.yml.
+    // Written to logs/software_versions.yml alongside the trace file.
+    ch_versions
+        .unique()
+        .collectFile(
+            name:     'software_versions.yml',
+            storeDir: "${launchDir}/logs/nextflow",
+            newLine:  true
+        )
 }
 

modules/local/antismash_run.nf

@@ -1,25 +1,19 @@
 process ANTISMASH_RUN {
     label 'antismash'
+    label 'process_medium'
     tag "${meta.id}"
 
-    cpus   8
-    memory '16 GB'
-    time   '60h'
-
-    publishDir "${params.target}", mode: 'copy', overwrite: true
-
     input:
     val(meta)
 
     output:
-    tuple val(meta), path("${meta.id}/antismash_local/**")
+    tuple val(meta), path("${meta.id}/antismash_local/**"), emit: results
+    path 'versions.yml',                                    emit: versions
 
     script:
     def out = meta.id
     def gbk = "${params.target}/${out}/predict_results/${out}.gbk"
     """
-    # Accept a compressed prediction (.gbk.gz); antismash needs it uncompressed, so
-    # inflate a local copy in the work dir when only the gzipped form is present.
     GBK="${gbk}"
     if [ ! -f "\$GBK" ] && [ -f "${gbk}.gz" ]; then
         zcat "${gbk}.gz" > ${out}.predict.gbk
@@ -38,6 +32,11 @@ process ANTISMASH_RUN {
         -c ${task.cpus} \\
         \$GBK
     pigz ${out}/antismash_local/*.json
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        antismash: \$(antismash --version 2>&1 | grep -oP '(?<=antiSMASH )\\S+' || antismash --version 2>&1 | head -1)
+    END_VERSIONS
     """
 
     stub:
@@ -46,5 +45,9 @@ process ANTISMASH_RUN {
     mkdir -p ${out}/antismash_local
     touch ${out}/antismash_local/${out}.json.gz
     touch ${out}/antismash_local/index.html
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        antismash: 7.1.0
+    END_VERSIONS
     """
 }

modules/local/asm_stats.nf

@@ -1,29 +1,16 @@
-/*
- * asm_stats — Generate assembly statistics for clean genomes
- *
- * This module generates asm_stats.tsv with columns: ASMID, total_length_bp, N50_bp, contig_count.
- * Stats are used by earlgrey_mask.nf to select representative genomes per species (SELECT_REPS).
- *
- * Include in your workflow:
- *   include { ASM_STATS } from './modules/asm_stats'
- *   ASM_STATS(samples_csv, genome_dir)
- */
-
 process ASM_STATS {
     label 'setup'
+    label 'process_low'
 
     storeDir { params.tables_dir }
 
-    cpus   4
-    memory '8 GB'
-    time   '2h'
-
     input:
     path samples
     path genome_dir
 
     output:
     path 'asm_stats.tsv.gz', emit: stats
+    path 'versions.yml',     emit: versions
 
     script:
     """
@@ -34,12 +21,10 @@ process ASM_STATS {
 
     printf 'ASMID\\ttotal_length_bp\\tN50_bp\\tcontig_count\\n' > \$TMPFILE
 
-    # Extract ASMIDs from samples.csv
     awk -F',' 'NR>1 {print \$2}' ${samples} | sort -u | while read asmid; do
         [ -z "\$asmid" ] && continue
-        asmid="\$(echo "\$asmid" | xargs)"  # trim whitespace
+        asmid="\$(echo "\$asmid" | xargs)"
 
-        # Look for genome file: prefer .fa.gz, fall back to .fa, then .masked.fasta.gz
         if [ -f "${genome_dir}/\${asmid}.fa.gz" ]; then
             genome="${genome_dir}/\${asmid}.fa.gz"
         elif [ -f "${genome_dir}/\${asmid}.fa" ]; then
@@ -53,7 +38,6 @@ process ASM_STATS {
             continue
         fi
 
-        # Use seqkit to compute stats
         total_bp=\$(seqkit stats -T "\$genome" 2>/dev/null | tail -n 1 | awk '{print \$4}')
         n50=\$(seqkit fx2tab -l "\$genome" 2>/dev/null | sort -rn -k2 | \\
             awk -v total="\$total_bp" 'BEGIN{sum=0} {sum+=\$2; if(sum >= total/2) {print \$2; exit}}')
@@ -67,12 +51,19 @@ process ASM_STATS {
     done
 
     pigz -c \$TMPFILE > asm_stats.tsv.gz
-    echo "[INFO] Assembly statistics written: asm_stats.tsv.gz"
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        seqkit: \$(seqkit version 2>&1 | sed 's/seqkit v//')
+    END_VERSIONS
     """
 
     stub:
     """
     printf 'ASMID\\ttotal_length_bp\\tN50_bp\\tcontig_count\\n' | pigz -c > asm_stats.tsv.gz
-    echo "[STUB] ASM_STATS"
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        seqkit: 2.8.0
+    END_VERSIONS
     """
 }

modules/local/interproscan_run.nf

@@ -1,19 +1,14 @@
-// IPRSCAN5
 process INTERPROSCAN_RUN {
     label 'interproscan'
+    label 'process_medium'
     tag "${meta.id}"
 
-    cpus   8
-    memory '32 GB'
-    time   '60h'
-
-    publishDir "${params.target}", mode: 'copy', overwrite: true
-
     input:
     val(meta)
 
     output:
-    tuple val(meta), path("${meta.id}/annotate_misc/iprscan.xml")
+    tuple val(meta), path("${meta.id}/annotate_misc/iprscan.xml"), emit: results
+    path 'versions.yml',                                            emit: versions
 
     script:
     def out      = meta.id
@@ -26,12 +21,21 @@ process INTERPROSCAN_RUN {
     mkdir -p ${out}/annotate_misc
     interproscan.sh -i ${proteins} -f XML -o ${out}/annotate_misc/iprscan.xml \\
         -dp -goterms -pa -t p -cpu ${task.cpus}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        interproscan: \$(interproscan.sh --version 2>&1 | grep -oP '\\d+\\.\\d+\\.\\d+' | head -1)
+    END_VERSIONS
     """
 
     stub:
     def out = meta.id
     """
     mkdir -p ${out}/annotate_misc
     touch ${out}/annotate_misc/iprscan.xml
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        interproscan: 5.65-97.0
+    END_VERSIONS
     """
 }

modules/local/signalp_run.nf

@@ -1,18 +1,14 @@
 process SIGNALP_RUN {
     label 'signalp'
+    label 'process_medium'
     tag "${meta.id}"
 
-    cpus   8
-    memory '16 GB'
-    time   '12h'
-
-    publishDir "${params.target}", mode: 'copy', overwrite: true
-
     input:
     val(meta)
 
     output:
-    tuple val(meta), path("${meta.id}/annotate_misc/signalp.results.txt")
+    tuple val(meta), path("${meta.id}/annotate_misc/signalp.results.txt"), emit: results
+    path 'versions.yml',                                                    emit: versions
 
     script:
     def out      = meta.id
@@ -30,12 +26,21 @@ process SIGNALP_RUN {
     mkdir -p ${out}/annotate_misc
     cp \$TMPDIR/${out}_signalp/prediction_results.txt ${out}/annotate_misc/signalp.results.txt
     rm -rf \$TMPDIR/${out}_signalp
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        signalp: \$(signalp6 --version 2>&1 | grep -oP '\\d+\\.\\d+\\S*' | head -1)
+    END_VERSIONS
     """
 
     stub:
     def out = meta.id
     """
     mkdir -p ${out}/annotate_misc
     touch ${out}/annotate_misc/signalp.results.txt
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        signalp: 6.0g
+    END_VERSIONS
     """
 }

nextflow.config

@@ -65,6 +65,10 @@ params {
     help       = false
 }
 
+// ── Base resource tiers + per-module publishDir (applied before profiles) ─────
+includeConfig 'conf/base.config'
+includeConfig 'conf/modules.config'
+
 // ── Process defaults (apply to every process, every profile) ──────────────────
 process {
     shell          = ['/bin/bash', '-l']