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21 lines
795 B
Text
21 lines
795 B
Text
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { SEQUENZAUTILS_BAM2SEQZ } from '../../../../software/sequenzautils/bam2seqz/main.nf' addParams( options: [:] )
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workflow test_sequenzautils_bam2seqz {
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tumourbam = file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
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normalbam = file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true)
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input = [ [ id:'test' ], // meta map
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tumourbam,
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normalbam
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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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wigfile = file(params.test_data['sarscov2']['genome']['test_wig_gz'], checkIfExists: true)
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SEQUENZAUTILS_BAM2SEQZ ( input, fasta, wigfile )
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}
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