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18 lines
749 B
Text
18 lines
749 B
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { GATK4_SPLITNCIGARREADS } from '../../../../software/gatk4/splitncigarreads/main.nf' addParams( options: [:] )
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workflow test_gatk4_splitncigarreads {
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def input = []
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input = [ [ id:'test' ], // meta map
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[ file("${launchDir}/tests/data/bam/sarscov2_aln.bam", checkIfExists: true)] ]
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fasta = file("tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.fna", checkIfExists: true)
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fai = file("tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.fna.fai", checkIfExists: true)
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dict = file("tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.dict", checkIfExists: true)
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GATK4_SPLITNCIGARREADS ( input, fasta, fai, dict )
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}
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