Address review feedback from #1838 (Vag)#1840
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Three actionable points from Vag's #1838 review: - Lowercase Channel.x -> channel.x in local test files and workflows/rnaseq/main.nf. nf-core component changes deferred (would need an upstream PR per file) - pipeline_completion test: pin params.outdir = "${outputDir}" so Nextflow's report/timeline/trace/dag files (wired against params.outdir in nextflow.config) land in the nf-test sandbox instead of a literal null/pipeline_info/ directory. Verified on the VM - Populate the previously empty "Pipeline specific contribution guidelines" section in docs/CONTRIBUTING.md with rnaseq-specific notes: test profiles, CI skip env vars, test data sources, module conventions, .nftignore, snapshots, version-reporting topic, --genome catalogues, CHANGELOG style Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Picks up the actionable points from @vagkaratzas's review on #1838.
Channel.x→channel.xin local codeVag flagged a few
Channel.ofleftovers and asked whethernextflow lintwould catch them (it does). Lowercased every uppercaseChannel.reference in local test files (subworkflows/local/align_star/tests/*,subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.pipeline_completion.workflow.nf.test,modules/local/star_genomeparams_upgrade/tests/main.nf.test) and the one inworkflows/rnaseq/main.nf.nf-core/components are deliberately untouched - those would need upstream PRs and SHA bumps vianf-core modules update, which is out of scope here.outputDirin thePIPELINE_COMPLETIONtestVag asked whether
input[3] = "${outputDir}"in the pipeline_completion test was actually scoped to the nf-test sandbox or leaking to pipeline-level. Verified on the VM:${outputDir}is the per-test sandbox (.nf-test/tests/<id>/output), good.outdirworkflow input is consumed bycompletionEmail()only whenemail || email_on_failis set. Both are null in this test, soinput[3]is unused on this code path.nextflow.configwiresreport.file,timeline.file,trace.file,dag.fileagainstparams.outdir, which is null at the test level. That's why a literalnull/pipeline_info/directory was being created in the test sandbox.Fix: add a
params { outdir = "${outputDir}" }block to the test so the Nextflow execution reports land inoutput/pipeline_info/instead. Verified thenull/directory no longer appears post-fix and the test still passes.docs/CONTRIBUTING.mdReplaced the empty
<!-- TODO nf-core: ... -->placeholder under "Pipeline specific contribution guidelines" with rnaseq-specific notes: test profile families, CI skip env vars (SKIP_GPU/SKIP_SENTIEON/SKIP_PARABRICKS), test data sources, the "edit nf-core modules upstream, not in-tree" rule,conf/modules/config split, version-reporting topic (and the templated-module exception),--genomecatalogues, snapshot conventions, and.nftignore. Kept it tight, no walls of prose.CHANGELOG
Adds a #1840 entry under the 3.26.0 release section.
Test plan
pipeline_completiontest passes on VM, nonull/diralign_startests (rg, extra_args) pass on VM afterChannel.x→channel.xrewritestar_genomeparams_upgrademodule tests pass on VM🤖 Generated with Claude Code