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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
30 lines
1,006 B
Text
30 lines
1,006 B
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { VCF2MAF } from '../../../modules/vcf2maf/main.nf'
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include { UNTAR } from '../../../modules/untar/main.nf'
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workflow test_vcf2maf_no_vep {
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input_vcf = [
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[ id:'test' ],
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file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true)
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]
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fasta = [ file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ]
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VCF2MAF ( input_vcf, fasta, [] )
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}
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workflow test_vcf2maf_vep {
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input_vcf = [
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[ id:'test' ],
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file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true)
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]
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fasta = [ file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ]
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vep_cache = [ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['vep_cache'], checkIfExists: true) ]
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vep_cache_unpacked = UNTAR(vep_cache).untar.map { it[1] }
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VCF2MAF ( input_vcf, fasta, vep_cache_unpacked)
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}
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