haplotyper-battle-royale/modules/viquas/main.nf

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process VIQUAS {
tag "${prefix}"
label 'process_high'
label 'viquas'
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container 'code.millironx.com/millironx/haplotyper-battle-royale:viquas'
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input:
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tuple val(prefix), path(bam), path(bai)
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path(reference)
output:
tuple val(prefix), path("*.fa")
publishDir "${params.outdir}/${task.process}", mode: 'copy'
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when:
task.ext.when == null || task.ext.when
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script:
"""
viquas \\
${reference} \\
${bam}
"""
}