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b5825fe6b3
* Mpileup also likes intervals * Also update meta yml with inclusive input and intervals Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
25 lines
968 B
Text
25 lines
968 B
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { SAMTOOLS_MPILEUP } from '../../../../modules/samtools/mpileup/main.nf'
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workflow test_samtools_mpileup {
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input = [ [ id:'test', single_end:false ], // 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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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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SAMTOOLS_MPILEUP ( input, fasta )
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}
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workflow test_samtools_mpileup_intervals {
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input = [ [ id:'test', single_end:false ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
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file(params.test_data['sarscov2']['genome']['test_bed'], 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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SAMTOOLS_MPILEUP ( input, fasta )
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}
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