test: load prokaryotic config in nf-test instead of duplicating params#1736
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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 <noreply@anthropic.com>
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Warning Newer version of the nf-core template is available. Your pipeline is using an old version of the nf-core template: 3.5.1. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
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Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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Note that we don't have per-test profile config in CI, hence this workaround |
adamrtalbot
approved these changes
Feb 27, 2026
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. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Remove bigwig-related entries (BEDTOOLS_GENOMECOV_FW/REV, UCSC_BEDCLIP/BEDGRAPHTOBIGWIG, bigwig file paths) from the star_salmon prokaryotic snapshot since skip_bigwig=true is now applied via the prokaryotic config. Task count 58 -> 46. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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Summary
Addresses @adamrtalbot's PR #1717 feedback that prokaryotic nf-tests should not re-set params already defined in the prokaryotic profile.
Adds
config "../conf/prokaryotic.config"at thenextflow_pipelinelevel intests/prokaryotic.nf.test, so prokaryotic-specific settings are loaded from the config file rather than duplicated in each test's params block.Removed from params blocks (now inherited from
conf/prokaryotic.config):prokaryotic = truegffread_transcript_fasta = truealigner = 'bowtie2_salmon'featurecounts_feature_type = 'CDS'skip_rseqc,skip_dupradar,skip_qualimapskip_bigwigKept in params blocks (test-specific):
aligner = 'star_salmon'override for star_salmon testsskip_bbsplit,skip_preseq,skip_biotype_qc,skip_deseq2_qcmin_trimmed_reads = 0Follows up on #1734 which composed
test_prokaryoticonprokaryoticinnextflow.config.Test plan
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