27 lines
550 B
Text
27 lines
550 B
Text
process SHORAH_AMPLICON {
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tag "${prefix}"
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label 'process_high'
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label 'shorah'
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container 'quay.io/biocontainers/shorah:1.99.2--py38h73782ee_8'
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input:
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tuple val(prefix), path(bam), path(bai)
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path(reference)
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output:
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tuple val(prefix), path("*.vcf")
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tuple val(prefix), path("*support.fas")
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publishDir "${params.outdir}/${task.process}", mode: 'copy'
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when:
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task.ext.when == null || task.ext.when
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script:
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"""
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shorah amplicon \\
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-f ${reference} \\
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-b ${bam} \\
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"""
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}
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