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33 lines
1.6 KiB
Text
33 lines
1.6 KiB
Text
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { GATK4_APPLYBQSR } from '../../../../software/gatk4/applybqsr/main.nf' addParams( options: [:] )
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workflow test_gatk4_applybqsr {
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def input = []
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input = [ [ id:'test' ], // meta map
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file("${launchDir}/tests/data/genomics/sarscov2/bam/test_paired_end.sorted.bam", checkIfExists: true),
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file("${launchDir}/tests/data/genomics/sarscov2/table/test.table", checkIfExists: true) ]
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fasta = file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true)
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fastaidx = file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta.fai", checkIfExists: true)
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dict = file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.dict", checkIfExists: true)
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GATK4_APPLYBQSR ( input, fasta, fastaidx, dict, [] )
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}
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workflow test_gatk4_applybqsr_intervals {
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def input = []
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input = [ [ id:'test' ], // meta map
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file("${launchDir}/tests/data/genomics/sarscov2/bam/test_paired_end.sorted.bam", checkIfExists: true),
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file("${launchDir}/tests/data/genomics/sarscov2/table/test.table", checkIfExists: true) ]
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fasta = file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true)
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fastaidx = file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta.fai", checkIfExists: true)
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dict = file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.dict", checkIfExists: true)
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intervals = file("${launchDir}/tests/data/genomics/sarscov2/bed/test.bed", checkIfExists: true)
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GATK4_APPLYBQSR ( input, fasta, fastaidx, dict, intervals)
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}
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