Move self-contained channel construction into PIPELINE_INITIALISATION#1032
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erikrikarddaniel wants to merge 5 commits into
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Move self-contained channel construction into PIPELINE_INITIALISATION#1032erikrikarddaniel wants to merge 5 commits into
erikrikarddaniel wants to merge 5 commits into
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The stub: block referenced ${outformat} in the process output glob but
never assigned it (only script: did), so -stub-run failed with "No such
variable: outformat". Assign it in stub: the same way script: does, and
use it in the stub output filenames for consistency with the declared
output pattern. Patch regenerated via `nf-core modules patch cutadapt`.
Part of nf-core#1029: params used only to build a channel, with no other logic depending on how that channel is constructed, should be built once in PIPELINE_INITIALISATION and threaded down as explicit arguments rather than workflows/ampliseq.nf reaching into global params directly. Moves 9 such channels (metadata, report_template/css/logo/abstract, pplace_sheet's initial value, expected_sequences/abundances, metadata_category) through PIPELINE_INITIALISATION -> NFCORE_AMPLISEQ -> AMPLISEQ via take:/emit:. Behavior is unchanged; this is a pure plumbing refactor covered by the existing nf-test snapshot suite. Adds a second test case to tests/default.nf.test for --report_abstract and --metadata_category, the two params among these that weren't exercised by any existing test profile. Deliberately out of scope (left for follow-up): the ~90 remaining scalar params.X reads in workflows/ampliseq.nf, the 6 per-classifier reference-taxonomy channels (entangled with catalog-download logic), and params.X reaches inside subworkflows/local and modules/local.
erikrikarddaniel
marked this pull request as draft
July 24, 2026 18:05
nf-core core-team consensus is not to allow CLAUDE.md files in pipeline repos, to avoid this ballooning for other agents and cluttering the repo root. AGENTS.md remains as the single, tool-agnostic instructions file; agent-specific loading (e.g. Claude Code treating an AGENTS.md as if it were a CLAUDE.md) is configured per-user outside the repo instead.
erikrikarddaniel
marked this pull request as ready for review
July 24, 2026 21:30
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PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).Description
Part of #1029: moves the params that are used only to construct a channel (with no other logic depending on how it's built) out of
workflows/ampliseq.nfand intoPIPELINE_INITIALISATION, threading them down throughNFCORE_AMPLISEQ->AMPLISEQas explicittake:/emit:arguments instead of reaching into globalparamsdirectly.metadata,report_template/report_css/report_logo/report_abstract,pplace_sheet's initial value,expected_sequences/expected_abundances,metadata_category.tests/default.nf.testfor--report_abstractand--metadata_category, the two params among these that weren't exercised by any existing test profile.cutadaptmodule'sstub:block referenced${outformat}without ever assigning it (onlyscript:did), breaking-stub-run.Deliberately out of scope for this PR (left for follow-up): the remaining scalar
params.Xreads inworkflows/ampliseq.nf, the per-classifier reference-taxonomy channels (entangled with catalog-download logic), andparams.Xreaches insidesubworkflows/localandmodules/local.Verified:
nf-test(both cases pass, no snapshot changes),nf-core pipelines lint,nextflow lint .at 26.04.0 and 26.04.6 (0 errors both),prek run -a.