nf-core_modules/modules/dshbio/exportsegments/main.nf
2022-04-09 11:13:47 -05:00

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process DSHBIO_EXPORTSEGMENTS {
tag "${meta.id}"
label 'process_medium'
conda (params.enable_conda ? "bioconda::dsh-bio=2.0.8" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.8--hdfd78af_0' :
'quay.io/biocontainers/dsh-bio:2.0.8--hdfd78af_0' }"
input:
tuple val(meta), path(gfa)
output:
tuple val(meta), path("*.fa.gz"), emit: fasta
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}"
"""
dsh-bio \\
export-segments \\
$args \\
-i $gfa \\
-o ${prefix}.fa.gz
cat <<-END_VERSIONS > versions.yml
"${task.process}":
dshbio: \$(dsh-bio --version 2>&1 | grep -o 'dsh-bio-tools .*' | cut -f2 -d ' ')
END_VERSIONS
"""
}