From 6b7603697ca10c81b883487a15e6ccf7c6f0bc23 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Fri, 27 Feb 2026 12:57:48 +0000 Subject: [PATCH 1/4] test: load prokaryotic config in nf-test instead of duplicating params Add config "../conf/prokaryotic.config" to the prokaryotic test suite so that prokaryotic-specific settings (prokaryotic flag, aligner, gffread, featurecounts_feature_type, skip_bigwig, skip_rseqc, skip_dupradar, skip_qualimap) come from the profile config rather than being duplicated in each test's params block. Tests now only set: - Test data paths (input, fasta, gff, gtf=null, etc.) - Aligner override for star_salmon tests - Test-specific skips (bbsplit, preseq, biotype_qc, deseq2_qc) - min_trimmed_reads = 0 Addresses review feedback from @adamrtalbot in PR #1717. Co-Authored-By: Claude Opus 4.6 --- tests/prokaryotic.nf.test | 83 +++++++++++---------------------------- 1 file changed, 23 insertions(+), 60 deletions(-) diff --git a/tests/prokaryotic.nf.test b/tests/prokaryotic.nf.test index 46accfe92..c9cd7bb40 100644 --- a/tests/prokaryotic.nf.test +++ b/tests/prokaryotic.nf.test @@ -2,6 +2,7 @@ nextflow_pipeline { name "Test pipeline with prokaryotic settings" script "../main.nf" + config "../conf/prokaryotic.config" tag "pipeline" tag "prokaryotic" @@ -21,23 +22,15 @@ nextflow_pipeline { transcript_fasta = null additional_fasta = null - // Prokaryotic-specific settings - prokaryotic = true - gffread_transcript_fasta = true + // Override aligner (prokaryotic profile defaults to bowtie2_salmon) aligner = 'star_salmon' - featurecounts_feature_type = 'CDS' - // Skip eukaryote-specific QC tools - skip_rseqc = true - skip_dupradar = true - skip_qualimap = true + // Skip steps not needed for minimal testing + skip_bbsplit = true + skip_preseq = true skip_biotype_qc = true - skip_deseq2_qc = true - - // Skip unnecessary steps for faster testing - skip_bbsplit = true - skip_preseq = true - pseudo_aligner = null + skip_deseq2_qc = true + pseudo_aligner = null min_trimmed_reads = 0 } } @@ -77,23 +70,15 @@ nextflow_pipeline { transcript_fasta = null additional_fasta = null - // Prokaryotic-specific settings - prokaryotic = true - gffread_transcript_fasta = true + // Override aligner (prokaryotic profile defaults to bowtie2_salmon) aligner = 'star_salmon' - featurecounts_feature_type = 'CDS' - // Skip eukaryote-specific QC tools - skip_rseqc = true - skip_dupradar = true - skip_qualimap = true + // Skip steps not needed for minimal testing + skip_bbsplit = true + skip_preseq = true skip_biotype_qc = true - skip_deseq2_qc = true - - // Skip unnecessary steps for faster testing - skip_bbsplit = true - skip_preseq = true - pseudo_aligner = null + skip_deseq2_qc = true + pseudo_aligner = null min_trimmed_reads = 0 } } @@ -135,23 +120,12 @@ nextflow_pipeline { transcript_fasta = null additional_fasta = null - // Prokaryotic-specific settings - gffread_transcript_fasta = true - aligner = 'bowtie2_salmon' - skip_bigwig = true - featurecounts_feature_type = 'CDS' - - // Skip eukaryote-specific QC tools - skip_rseqc = true - skip_dupradar = true - skip_qualimap = true + // Skip steps not needed for minimal testing + skip_bbsplit = true + skip_preseq = true skip_biotype_qc = true - skip_deseq2_qc = true - - // Skip unnecessary steps for faster testing - skip_bbsplit = true - skip_preseq = true - pseudo_aligner = null + skip_deseq2_qc = true + pseudo_aligner = null min_trimmed_reads = 0 } } @@ -191,23 +165,12 @@ nextflow_pipeline { transcript_fasta = null additional_fasta = null - // Prokaryotic-specific settings - gffread_transcript_fasta = true - aligner = 'bowtie2_salmon' - skip_bigwig = true - featurecounts_feature_type = 'CDS' - - // Skip eukaryote-specific QC tools - skip_rseqc = true - skip_dupradar = true - skip_qualimap = true + // Skip steps not needed for minimal testing + skip_bbsplit = true + skip_preseq = true skip_biotype_qc = true - skip_deseq2_qc = true - - // Skip unnecessary steps for faster testing - skip_bbsplit = true - skip_preseq = true - pseudo_aligner = null + skip_deseq2_qc = true + pseudo_aligner = null min_trimmed_reads = 0 } } From e3d546958ebaa8c3581496d7b3fbcba85e272122 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Fri, 27 Feb 2026 13:01:39 +0000 Subject: [PATCH 2/4] docs: add PR #1736 to changelog Co-Authored-By: Claude Opus 4.6 --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0a2c0010f..33b7da3e7 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -57,6 +57,7 @@ Special thanks to the following for their contributions to the release: - [PR #1730](https://github.com/nf-core/rnaseq/pull/1730) - Bump Nextflow from 25.04.0 to 25.04.3 in CI to fix `conda create --mkdir` failure ([nextflow-io/nextflow#5947](https://github.com/nextflow-io/nextflow/issues/5947)) - [PR #1734](https://github.com/nf-core/rnaseq/pull/1734) - Compose `test_prokaryotic` profile on `prokaryotic` to remove duplicated settings - [PR #1735](https://github.com/nf-core/rnaseq/pull/1735) - Code quality improvements: replace opaque tuple indexing with named destructuring, rename `ch_dummy_file`, move metro map docs, align GPU CI workflow with other workflows +- [PR #1736](https://github.com/nf-core/rnaseq/pull/1736) - Load prokaryotic config in nf-test instead of duplicating params in each test ### Parameters From 4e5e748155f807edea161b8f12c5329d542d48fe Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Fri, 27 Feb 2026 13:11:44 +0000 Subject: [PATCH 3/4] test: remove prokaryotic snapshots for regeneration The prokaryotic config now applies skip_bigwig = true to all prokaryotic tests (including star_salmon), which is correct behavior but changes the expected output. Removing snapshots so CI regenerates them. 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Task count 58 -> 46. 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