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28 lines
744 B
Text
28 lines
744 B
Text
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { SAMTOOLS_COLLATE } from '../../../../modules/samtools/collate/main.nf'
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workflow test_samtools_collate {
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input = [
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[ id:'test', single_end:false ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
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]
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SAMTOOLS_COLLATE ( input, [] )
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}
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workflow test_samtools_collate_cram {
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input = [
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[ id:'test', single_end:false ], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true)
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]
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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SAMTOOLS_COLLATE ( input, fasta )
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}
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