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44 lines
1.5 KiB
Text
44 lines
1.5 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { IVAR_VARIANTS } from '../../../../software/ivar/variants/main.nf' addParams([:])
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workflow test_ivar_variants_no_gff_no_mpileup {
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params.gff = false
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params.save_mpileup = false
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input = [ [ 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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dummy = file("dummy_file.txt")
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IVAR_VARIANTS ( input, fasta, dummy )
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}
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workflow test_ivar_variants_no_gff_with_mpileup {
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params.gff = false
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params.save_mpileup = true
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input = [ [ 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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dummy = file("dummy_file.txt")
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IVAR_VARIANTS ( input, fasta, dummy )
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}
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workflow test_ivar_variants_with_gff_with_mpileup {
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params.gff = true
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params.save_mpileup = true
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input = [ [ 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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gff = file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true)
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IVAR_VARIANTS ( input, fasta, gff )
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}
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