mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 21:53:10 +00:00
50 lines
1.6 KiB
Text
50 lines
1.6 KiB
Text
|
// Import generic module functions
|
||
|
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
||
|
|
||
|
params.options = [:]
|
||
|
options = initOptions(params.options)
|
||
|
|
||
|
process CHECKM_LINEAGEWF {
|
||
|
tag "$meta.id"
|
||
|
label 'process_medium'
|
||
|
publishDir "${params.outdir}",
|
||
|
mode: params.publish_dir_mode,
|
||
|
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||
|
|
||
|
conda (params.enable_conda ? "bioconda::checkm-genome=1.1.3" : null)
|
||
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||
|
container "https://depot.galaxyproject.org/singularity/checkm-genome:1.1.3--py_1"
|
||
|
} else {
|
||
|
container "quay.io/biocontainers/checkm-genome:1.1.3--py_1"
|
||
|
}
|
||
|
|
||
|
input:
|
||
|
tuple val(meta), path(fasta)
|
||
|
val fasta_ext
|
||
|
|
||
|
output:
|
||
|
tuple val(meta), path("${prefix}") , emit: checkm_output
|
||
|
tuple val(meta), path("${prefix}.tsv"), emit: checkm_tsv
|
||
|
path "versions.yml" , emit: versions
|
||
|
|
||
|
script:
|
||
|
prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||
|
"""
|
||
|
checkm \\
|
||
|
lineage_wf \\
|
||
|
-t $task.cpus \\
|
||
|
-f ${prefix}.tsv \\
|
||
|
--tab_table \\
|
||
|
--pplacer_threads $task.cpus \\
|
||
|
-x $fasta_ext \\
|
||
|
$options.args \\
|
||
|
. \\
|
||
|
$prefix
|
||
|
|
||
|
cat <<-END_VERSIONS > versions.yml
|
||
|
${getProcessName(task.process)}:
|
||
|
${getSoftwareName(task.process)}: \$( checkm 2>&1 | grep '...:::' | sed 's/.*CheckM v//;s/ .*//' )
|
||
|
END_VERSIONS
|
||
|
"""
|
||
|
}
|