mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
906577873b
* New functions.nf * Convert code to create versions.yml * Update meta.yml * update output channel * Fix more meta.yml * Manually update remaining modules * remove superflous echo * Fix misformatted meta.yml files * Fix yaml, was list instead of dict * fix version for bcftools Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
51 lines
1.6 KiB
Text
51 lines
1.6 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
|
|
|
params.options = [:]
|
|
options = initOptions(params.options)
|
|
|
|
process QUAST {
|
|
label 'process_medium'
|
|
publishDir "${params.outdir}",
|
|
mode: params.publish_dir_mode,
|
|
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
|
|
|
|
conda (params.enable_conda ? 'bioconda::quast=5.0.2' : null)
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
|
container 'https://depot.galaxyproject.org/singularity/quast:5.0.2--py37pl526hb5aa323_2'
|
|
} else {
|
|
container 'quay.io/biocontainers/quast:5.0.2--py37pl526hb5aa323_2'
|
|
}
|
|
|
|
input:
|
|
path consensus
|
|
path fasta
|
|
path gff
|
|
val use_fasta
|
|
val use_gff
|
|
|
|
output:
|
|
path "${prefix}" , emit: results
|
|
path '*.tsv' , emit: tsv
|
|
path "versions.yml" , emit: version
|
|
|
|
script:
|
|
def software = getSoftwareName(task.process)
|
|
prefix = options.suffix ?: software
|
|
def features = use_gff ? "--features $gff" : ''
|
|
def reference = use_fasta ? "-r $fasta" : ''
|
|
"""
|
|
quast.py \\
|
|
--output-dir $prefix \\
|
|
$reference \\
|
|
$features \\
|
|
--threads $task.cpus \\
|
|
$options.args \\
|
|
${consensus.join(' ')}
|
|
ln -s ${prefix}/report.tsv
|
|
cat <<-END_VERSIONS > versions.yml
|
|
${getProcessName(task.process)}:
|
|
${getSoftwareName(task.process)}: \$(quast.py --version 2>&1 | sed 's/^.*QUAST v//; s/ .*\$//')
|
|
END_VERSIONS
|
|
"""
|
|
}
|