mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
40 lines
1.2 KiB
Text
40 lines
1.2 KiB
Text
process AMPS {
|
|
label 'process_low'
|
|
|
|
conda (params.enable_conda ? "bioconda::hops=0.35" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/hops:0.35--hdfd78af_1' :
|
|
'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
|
|
|
|
when:
|
|
task.ext.when == null || task.ext.when
|
|
|
|
script:
|
|
def args = task.ext.args ?: ''
|
|
"""
|
|
postprocessing.AMPS.r \\
|
|
-r $maltextract_results \\
|
|
-n $taxon_list \\
|
|
-m $filter \\
|
|
-t $task.cpus \\
|
|
-j \\
|
|
$args
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
amps: \$(echo \$(hops --version 2>&1) | sed 's/HOPS version//')
|
|
END_VERSIONS
|
|
"""
|
|
}
|