2023-09-23 21:26:25 +00:00
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process HAPLINK_SEQUENCES {
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2023-09-23 21:27:17 +00:00
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tag "${method}: ${prefix}"
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2023-09-23 21:28:12 +00:00
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label 'process_single'
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2023-09-26 13:27:22 +00:00
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label 'haplink'
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2023-09-23 21:26:25 +00:00
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2023-09-30 21:01:09 +00:00
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container 'ghcr.io/ksumngs/haplink.jl:1.0.0'
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2023-09-23 21:28:57 +00:00
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2023-09-23 21:26:25 +00:00
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input:
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tuple val(prefix), val(method), path(yaml)
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path reference
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output:
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tuple val(prefix), val(method), path("*.fasta")
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2023-10-19 02:40:08 +00:00
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publishDir "${params.outdir}/${method}", mode: 'copy'
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2023-09-23 21:26:25 +00:00
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2023-09-26 13:27:22 +00:00
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when:
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task.ext.when == null || task.ext.when
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2023-09-23 21:26:25 +00:00
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script:
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"""
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export JULIA_NUM_THREADS=${task.cpus}
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haplink sequences \\
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"${reference}" \\
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"${yaml}" \\
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--prefix "${prefix}" \\
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> "${prefix}.fasta"
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"""
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}
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