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47 lines
1.6 KiB
Text
47 lines
1.6 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { IVAR_VARIANTS } from '../../../../modules/ivar/variants/main.nf'
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workflow test_ivar_variants_no_gff_no_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_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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fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
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gff = []
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save_mpileup = false
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IVAR_VARIANTS ( input, fasta, fai, gff, save_mpileup )
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}
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workflow test_ivar_variants_no_gff_with_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_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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fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
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gff = []
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save_mpileup = true
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IVAR_VARIANTS ( input, fasta, fai, gff, save_mpileup )
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}
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workflow test_ivar_variants_with_gff_with_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_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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fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
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gff = file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true)
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save_mpileup = true
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IVAR_VARIANTS ( input, fasta, fai, gff, save_mpileup )
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}
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