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https://github.com/MillironX/nf-core_modules.git
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bb90e4fb78
* Remove customisation from bcftools modules * Add save_mpileup option to bcftools/mpileup * Remove params.save_mpileup from ivar/consensus * Update meta.ymls
29 lines
883 B
Text
29 lines
883 B
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { BCFTOOLS_MPILEUP } from '../../../../modules/bcftools/mpileup/main.nf'
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workflow test_bcftools_mpileup {
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input = [
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[ id:'test' ], // meta map
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[ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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save_mpileup = false
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BCFTOOLS_MPILEUP ( input, fasta, save_mpileup )
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}
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workflow test_bcftools_save_mpileup {
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input = [
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[ id:'test' ], // meta map
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[ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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save_mpileup = true
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BCFTOOLS_MPILEUP ( input, fasta, save_mpileup )
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}
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