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

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process PREDICTHAPLO {
tag "${prefix}"
label 'process_high'
container 'quay.io/biocontainers/predicthaplo:2.1.4--h9b88814_5'
input:
tuple val(prefix), path(bam), path(bai)
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path(reference)
output:
tuple val(prefix), path("*.fa*")
publishDir "results/${task.process}", mode: 'copy'
script:
"""
predicthaplo \\
--sam "${bam}" \\
--reference "${reference}" \\
--prefix "${prefix}"
"""
}