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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
824 B
Text
29 lines
824 B
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { IVAR_CONSENSUS } from '../../../../modules/ivar/consensus/main.nf'
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workflow test_ivar_consensus {
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input = [
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[ id:'test'],
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file(params.test_data['sarscov2']['illumina']['test_paired_end_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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IVAR_CONSENSUS ( input, fasta, save_mpileup)
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}
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workflow test_ivar_consensus_mpileup {
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input = [
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[ id:'test'],
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file(params.test_data['sarscov2']['illumina']['test_paired_end_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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IVAR_CONSENSUS ( input, fasta, save_mpileup)
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}
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