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a90332906b
* add mergebamalignment * fix test.yml * update to latest gatk4 version * Update software/gatk4/mergebamalignment/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/data/README.md Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gatk4/mergebamalignment/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gatk4/mergebamalignment/meta.yml * fixed unmapped/unaligned Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
16 lines
769 B
Text
16 lines
769 B
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { GATK4_MERGEBAMALIGNMENT } from '../../../../software/gatk4/mergebamalignment/main.nf' addParams( options: [:] )
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workflow test_gatk4_mergebamalignment {
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def input = []
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input = [ [ id:'test' ], // meta map
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file("${launchDir}/tests/data/genomics/sarscov2/bam/test_single_end.bam", checkIfExists: true) ]
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unmapped = file("${launchDir}/tests/data/genomics/sarscov2/bam/test_unaligned.bam", checkIfExists: true)
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fasta = file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true)
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dict = file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.dict", checkIfExists: true)
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GATK4_MERGEBAMALIGNMENT ( input, unmapped, fasta, dict )
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}
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