nf-core_modules/modules/seacr/callpeak/main.nf
2022-02-04 09:53:32 +01:00

41 lines
1.4 KiB
Text

def VERSION = '1.3' // Version information not provided by tool on CLI
process SEACR_CALLPEAK {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::seacr=1.3 conda-forge::r-base=4.0.2 bioconda::bedtools=2.30.0" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-03bfeb32fe80910c231f630d4262b83677c8c0f4:f4bb19b68e66de27e4c64306f951d5ff11919931-0' :
'quay.io/biocontainers/mulled-v2-03bfeb32fe80910c231f630d4262b83677c8c0f4:f4bb19b68e66de27e4c64306f951d5ff11919931-0' }"
input:
tuple val(meta), path(bedgraph), path(ctrlbedgraph)
val (threshold)
output:
tuple val(meta), path("*.bed"), emit: bed
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def function_switch = ctrlbedgraph ? "$ctrlbedgraph" : "$threshold"
"""
SEACR_1.3.sh \\
$bedgraph \\
$function_switch \\
$args \\
$prefix
cat <<-END_VERSIONS > versions.yml
"${task.process}":
seacr: $VERSION
bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//')
END_VERSIONS
"""
}