mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 04:33:10 +00:00
daab0a77dd
* Update main.nf * Update meta.yml * Re-add logos as not staged in a way that works with MultiQC config files * Update main.nf * Remove now unnecessary input channel * Remove unused channel from tests * Update hAMRonization to 1.1.1 and add hAMRonization farGene * Fix hamronizatio ntests * Prettier * Fix fargene linting * Correct file * Fix fargene output * Apply suggestions from code review Co-authored-by: Jasmin F <73216762+jasmezz@users.noreply.github.com> * Fix summarise tests * Prettier Co-authored-by: Jasmin F <73216762+jasmezz@users.noreply.github.com>
43 lines
1.3 KiB
Text
43 lines
1.3 KiB
Text
process HAMRONIZATION_FARGENE {
|
|
tag "$meta.id"
|
|
label 'process_single'
|
|
|
|
conda (params.enable_conda ? "bioconda::hamronization=1.1.1" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/hamronization:1.1.1--pyhdfd78af_0':
|
|
'quay.io/biocontainers/hamronization:1.1.1--pyhdfd78af_0' }"
|
|
|
|
input:
|
|
tuple val(meta), path(report)
|
|
val(format)
|
|
val(software_version)
|
|
val(reference_db_version)
|
|
|
|
output:
|
|
tuple val(meta), path("*.json") , optional: true, emit: json
|
|
tuple val(meta), path("*.tsv") , optional: true, emit: tsv
|
|
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}"
|
|
"""
|
|
hamronize \\
|
|
fargene \\
|
|
${report} \\
|
|
$args \\
|
|
--format ${format} \\
|
|
--analysis_software_version ${software_version} \\
|
|
--reference_database_version ${reference_db_version} \\
|
|
--input_file_name ${prefix} \\
|
|
> ${prefix}.${format}
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
hamronization: \$(echo \$(hamronize --version 2>&1) | cut -f 2 -d ' ' )
|
|
END_VERSIONS
|
|
"""
|
|
}
|