hicpro2pairs.nf 1.09 KiB
process HICPRO2PAIRS {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::pairix=0.3.7" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/pairix:0.3.7--py36h30a8e3e_3' :
'quay.io/biocontainers/pairix:0.3.7--py36h30a8e3e_3' }"
input:
tuple val(meta), path(vpairs)
path chrsize
output:
tuple val(meta), path("*.pairs.gz"), path("*.pairs.gz.px2"), emit: pairs
path("versions.yml"), emit: versions
script:
prefix = "${meta.id}"
"""
##columns: readID chr1 pos1 chr2 pos2 strand1 strand2
awk '{OFS="\t";print \$1,\$2,\$3,\$5,\$6,\$4,\$7}' $vpairs | bgzip -c > ${prefix}_contacts.pairs.gz
##sort -k2,2 -k4,4 -k3,3n -k5,5n ${prefix}_contacts.pairs | bgzip -c > ${prefix}_contacts.pairs.gz
pairix -f ${prefix}_contacts.pairs.gz
cat <<-END_VERSIONS > versions.yml
"${task.process}":
pairix: \$(echo \$(pairix 2>&1 | grep Version | sed -e 's/Version: //'))
END_VERSIONS
"""
}