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

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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
"""
}