32 lines
695 B
Text
32 lines
695 B
Text
process HAPLINK_HAPLOTYPES {
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tag "${prefix}"
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label 'process_high'
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label 'haplink'
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container 'ghcr.io/ksumngs/haplink.jl:1.0.0'
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input:
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tuple val(prefix), path(bam), path(bai), path(vcf)
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path reference
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output:
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tuple val(prefix), path("*.yaml")
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publishDir "${params.outdir}/${task.process}", mode: 'copy'
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when:
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task.ext.when == null || task.ext.when
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script:
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def ml_args = task.ext.ml_args ?: ''
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"""
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export JULIA_NUM_THREADS=${task.cpus}
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haplink haplotypes \\
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"${reference}" \\
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"${vcf}" \\
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"${bam}" \\
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--frequency 0.01 \\
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${ml_args} \\
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> "${prefix}.yaml"
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"""
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}
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