24 lines
481 B
Text
24 lines
481 B
Text
process HAPLINK_VARIANTS {
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tag "${prefix}"
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label 'process_medium'
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container 'quay.io/biocontainers/haplink:1.0.0--h031d066_0'
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input:
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tuple val(prefix), path(bam), path(bai)
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path reference
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output:
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tuple val(prefix), path("*.vcf")
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publishDir "results", mode: 'copy'
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script:
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"""
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export JULIA_NUM_THREADS=${task.cpus}
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haplink variants \\
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"${reference}" \\
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"${bam}" \\
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> "${prefix}.vcf"
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"""
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}
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