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f19ec865aa
vcf2maf module created Additions: - vcf2maf module created - If VEP is present in PATH, it is added to command - If VEP is missing, it is ignored (recommended to skip with --inhibit-vep) - VEP version automatically added to versions.yml - Uses VEP cache during testing which is added to test-datasets in https://github.com/nf-core/test-datasets/pull/563 - Default Docker image includes VEP and vcf2maf - Test includes without VEP. Relates to #490
14 lines
519 B
Text
14 lines
519 B
Text
params.species = "homo_sapiens"
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params.build = "GRCh38"
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process {
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publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
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withName: 'test_vcf2maf_no_vep:VCF2MAF' {
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ext.args = "--ncbi-build ${params.build} --species ${params.species} --inhibit-vep"
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container = "quay.io/biocontainers/vcf2maf:1.6.21--hdfd78af_0"
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}
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withName: 'test_vcf2maf_vep:VCF2MAF' {
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ext.args = "--ncbi-build ${params.build} --species ${params.species}"
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}
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}
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