nf-test for subworkflows - I #695
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fellen31
reviewed
Apr 15, 2025
nf-test.config
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| // Include plugins | ||
| plugins { | ||
| load "nft-bam@0.4.0" |
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Perhaps
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| load "nft-bam@0.4.0" | |
| load "nft-bam@0.6.0" |
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| process { | |||
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| publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } | |||
| params { | ||
| aligner = 'bwamem2' | ||
| mt_aligner = 'bwamem2' | ||
| testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/' |
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Consider to set this in test.config, then using configFile "conf/test.config" in nf-test.config to skip this line for all tests.
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| workflow.out.genome_bam_bai.collect { meta, bamfile, index -> [ meta, bam(bamfile).getHeaderMD5(), index ] }, | ||
| workflow.out.mt_bam_bai.collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), index ] }, | ||
| workflow.out.mtshift_bam_bai.collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), index ] }, | ||
| workflow.out.versions |
| """ | ||
| input[0] = Channel.of([ | ||
| [id:'mt'], | ||
| file('https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference_mt.fa', checkIfExists: true) |
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Think you could use testdata_base_path in the setups if you set in it the config.
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| process { | |||
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| publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } | |||
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Suggested change
| publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } |
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| testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/' | ||
| fasta = params.testdata_base_path + 'reference.fasta' | ||
| fai = params.testdata_base_path + 'reference.fasta.fai' | ||
| dict = params.testdata_base_path + 'reference.dict' |
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Do you not need to set params.scatter_count?
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PR checklist
Renamed "test_one_sample" to "test_singleton"
Added tests for a few subworkflows.
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile test_one_sample,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).