Refactor/meta map#16
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Two config-layer changes:
1. Define params.genome_dir = "${launchDir}/input_clean_genomes" in
profile_annotate.config. It was referenced by the ASM_STATS call site
(funannotate.nf:2063) but never defined, so `-profile test -stub-run`
crashed with "Argument of file() function cannot be null" — i.e. CI on
main was red. The value matches GENOME_CLEAN's storeDir target and
earlgrey_mask.nf's identical param. Stub-run gate is now green (exit 0).
2. Rename the `module` provisioning profile to `ucr_hpcc` to mark it as an
institutional (site-specific Lmod) profile, the nf-core/configs model.
Portable runs use singularity/pixi. Updates nextflow.config, the renamed
conf/provision_ucr_hpcc.config header, run_annotate.sh default, and doc refs.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01BFGQVQDdSLEgpSJehG9qx5
…acking Rewrite REFACTORING_PLAN.md as the single source of truth: the meta-map data contract (Principle 0), target main.nf/workflows/subworkflows/modules layout, per-process extraction checklist gated on stub-run, corrected migration order, and the nf-core distance scorecard. Remove IMPLEMENTATION_SUMMARY.md and MODULE_STRUCTURE.txt — status reports that described aspiration as completed work and would rot. Add .github/REFACTOR_ISSUES.md (epic + 12 ordered issues) and the idempotent scripts/create_refactor_issues.sh that creates them via gh. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01BFGQVQDdSLEgpSJehG9qx5
Phase 0 (#3) groundwork — the only safe, standalone sub-step ahead of the atomic channel conversion: - Add SampleUtils.makeMeta(row): the single authoritative definition of the per-sample `meta` map, reproducing the funannotate.nf `jobs` channel cleaning field-for-field so wiring it in will be behaviour-preserving. Not yet called. - Promote the hardcoded header_length=24 constant to params.header_length (nextflow.config + nextflow_schema.json) — it is global, not per-sample, so it leaves the per-sample tuple in the conversion. - Document the atomic conversion recipe (shim technique + the position-coupled channel-op translations) in REFACTORING_PLAN.md Principle 0. No behaviour change: makeMeta is unused, header_length is still threaded through the tuple for now. Stub-run gate green (completed=16, failed=0). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01BFGQVQDdSLEgpSJehG9qx5
…l(meta), val/path(genome))
Replace the fragile positional 10-tuple
tuple(out, asmid, species, strain, locustag, busco, header_length, transl_table, gz, taxonid)
with the standard DSL2 meta-map contract on every process and every channel op.
Processes converted (shim: alias block at script top, input/output rewritten):
GENOME_CLEAN, GENOME_CLEAN_BATCH, MASKREPEAT_TANTAN_RUN, RNASEQ_PREPARE,
FUNANNOTATE_TRAIN, FUNANNOTATE_PREDICT, ANTISMASH_RUN, INTERPROSCAN_RUN,
SIGNALP_RUN, FUNANNOTATE_ANNOTATE, FUNANNOTATE_UPDATE
Workflow changes:
- jobs channel: per-field defs → SampleUtils.makeMeta(row), emits tuple(meta, gz)
- postpredict channel: same, emits just meta
- All ~40 channel ops updated: filter/map destructuring, species-keyed groupTuple/combine,
slice sentinels replaced, annotate chain simplified (meta-only)
- clean_genome_ch: uses it[0] index (not fixed-arity destructure) so the gate works
whether ifEmpty([]) contributes 0 or N elements to the combined sentinel
params.header_length (added in groundwork commit) now consumed in all processes;
removed from per-sample tuple entirely.
Stub-run gate: 13 completed, 0 failed (GENOME_CLEAN_BATCH + MASKREPEAT×2 +
FUNANNOTATE_PREDICT×2 + ANTISMASH×2 + INTERPROSCAN×2 + SIGNALP×2 + ANNOTATE×2).
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01AbWwmm9v6dJn13sgAJn3Sa
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