feat: addition of vembrane table module #9285
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| """ | ||
| input[0] = [ | ||
| [ id:'test', single_end:false ], // meta map | ||
| file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_vcf'], checkIfExists: true) |
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We moved to a different syntax for the test_data a little while ago, along the lines of file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) rather than the dictionary.
| process { | ||
| withName: 'VEMBRANE_TABLE' { | ||
| ext.args = params.vembrane_args ?: '' | ||
| ext.prefix = { params.vembrane_prefix ?: "${meta.id}" } |
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We don't normally test the prefix.
mkatsanto
moved this from To do
to Ready for review
in Hackathon Barcelona October 2025
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out).match() } |
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Can we get the version displayed explicitely once? :)
| { assert snapshot(process.out).match() } | |
| { assert snapshot( | |
| process.out, | |
| path(process.out.versions[0]).yaml | |
| ).match() } |
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this fix causes a syntax error
will update with { assert snapshot(process.out.versions).match("versions") }
update: snapshot was obsolete reimplementing
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huh this should not lead to an error
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snapshot was obsolete reimplementing
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nextflow lint -format -sort-declarations -spaces 4 -harshil-alignment modules/nf-core/vembrane/table/main.nf
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nextflow lint -format -sort-declarations -spaces 4 -harshil-alignment modules/nf-core/vembrane/table/main.nf
Nextflow linting complete!
✅ 1 file had no errors (1 formatted)
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github-project-automation
bot
moved this from Ready for review
to In progress
in Hackathon Barcelona October 2025
Co-authored-by: Famke Bäuerle <[email protected]>
Co-authored-by: Famke Bäuerle <[email protected]>
…into vembrane_table
5 participants
PR checklist
Fixes ##9265
versions.ymlfile.labelnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile conda