mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
46 lines
2 KiB
Text
46 lines
2 KiB
Text
process MERQURYFK_KATCOMP {
|
|
tag "$meta.id"
|
|
label 'process_medium'
|
|
|
|
if (params.enable_conda) {
|
|
error "Conda environments cannot be used when using the FastK tool. Please use docker or singularity containers."
|
|
}
|
|
// WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
|
|
container 'ghcr.io/nbisweden/fastk_genescopefk_merquryfk:1.0'
|
|
|
|
input:
|
|
tuple val(meta), path(fastk1_hist), path(fastk1_ktab), path(fastk2_hist), path(fastk2_ktab)
|
|
|
|
output:
|
|
tuple val(meta), path("*.fi.png"), emit: filled_png , optional: true
|
|
tuple val(meta), path("*.ln.png"), emit: line_png , optional: true
|
|
tuple val(meta), path("*.st.png"), emit: stacked_png, optional: true
|
|
tuple val(meta), path("*.fi.pdf"), emit: filled_pdf , optional: true
|
|
tuple val(meta), path("*.ln.pdf"), emit: line_pdf , optional: true
|
|
tuple val(meta), path("*.st.pdf"), emit: stacked_pdf, optional: true
|
|
path "versions.yml" , emit: versions
|
|
|
|
when:
|
|
task.ext.when == null || task.ext.when
|
|
|
|
script:
|
|
def args = task.ext.args ?: ''
|
|
def prefix = task.ext.prefix ?: "${meta.id}"
|
|
def FASTK_VERSION = 'f18a4e6d2207539f7b84461daebc54530a9559b0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
|
|
def MERQURY_VERSION = '8f3ab706e4cf4d7b7d1dfe5739859e3ebd26c494' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
|
|
"""
|
|
KatComp \\
|
|
$args \\
|
|
-T$task.cpus \\
|
|
${fastk1_ktab.find{ it.toString().endsWith(".ktab") }} \\
|
|
${fastk2_ktab.find{ it.toString().endsWith(".ktab") }} \\
|
|
$prefix
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
fastk: $FASTK_VERSION
|
|
merquryfk: $MERQURY_VERSION
|
|
r: \$( R --version | sed '1!d; s/.*version //; s/ .*//' )
|
|
END_VERSIONS
|
|
"""
|
|
}
|