nf-core_modules/modules/haplocheck/main.nf
2022-06-08 10:10:24 -03:00

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process HAPLOCHECK {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::haplocheck=1.3.3" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/haplocheck:1.3.3--h4a94de4_0':
'quay.io/biocontainers/haplocheck:1.3.3--h4a94de4_0' }"
input:
tuple val(meta), path(vcf)
output:
tuple val(meta), path("*.txt") , emit: txt
tuple val(meta), path("*.html"), emit: html
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
"""
haplocheck --raw --out $prefix $vcf
cat <<-END_VERSIONS > versions.yml
"${task.process}":
haplocheck: \$(echo \$(haplocheck --version 2>&1) | cut -f 2 -d " " )
END_VERSIONS
"""
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.raw.txt
touch ${prefix}.html
cat <<-END_VERSIONS > versions.yml
"${task.process}":
haplocheck: \$(echo \$(haplocheck --version 2>&1) | cut -f 2 -d " " )
END_VERSIONS
"""
}