mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-15 06:03:10 +00:00
7b3315591a
* Remove def software line * Replace version with versions in emit statement * Fix default software names
47 lines
1.6 KiB
Text
47 lines
1.6 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
|
|
|
params.options = [:]
|
|
options = initOptions(params.options)
|
|
|
|
process AMPS {
|
|
label 'process_low'
|
|
publishDir "${params.outdir}",
|
|
mode: params.publish_dir_mode,
|
|
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
|
|
|
|
conda (params.enable_conda ? "bioconda::hops=0.35" : null)
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
|
container "https://depot.galaxyproject.org/singularity/hops:0.35--hdfd78af_1"
|
|
} else {
|
|
container "quay.io/biocontainers/hops:0.35--hdfd78af_1"
|
|
}
|
|
|
|
input:
|
|
path maltextract_results
|
|
path taxon_list
|
|
val filter
|
|
|
|
output:
|
|
path "results/heatmap_overview_Wevid.json" , emit: json
|
|
path "results/heatmap_overview_Wevid.pdf" , emit: summary_pdf
|
|
path "results/heatmap_overview_Wevid.tsv" , emit: tsv
|
|
path "results/pdf_candidate_profiles/" , emit: candidate_pdfs
|
|
path "versions.yml" , emit: versions
|
|
|
|
script:
|
|
"""
|
|
postprocessing.AMPS.r \\
|
|
-r $maltextract_results \\
|
|
-n $taxon_list \\
|
|
-m $filter \\
|
|
-t $task.cpus \\
|
|
-j \\
|
|
$options.args
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
${getProcessName(task.process)}:
|
|
${getSoftwareName(task.process)}: \$(echo \$(hops --version 2>&1) | sed 's/HOPS version//')
|
|
END_VERSIONS
|
|
"""
|
|
}
|