nf-core_modules/modules/plasmidid/main.nf
Gregor Sturm 906577873b
Bulk update modules to use versions.yml (#739)
* 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>
2021-09-27 09:41:24 +01:00

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
params.options = [:]
options = initOptions(params.options)
process PLASMIDID {
tag "$meta.id"
label 'process_medium'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? 'bioconda::plasmidid=1.6.5' : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container 'https://depot.galaxyproject.org/singularity/plasmidid:1.6.5--hdfd78af_0'
} else {
container 'quay.io/biocontainers/plasmidid:1.6.5--hdfd78af_0'
}
input:
tuple val(meta), path(scaffold)
path fasta
output:
tuple val(meta), path("${prefix}/*final_results.html"), emit: html
tuple val(meta), path("${prefix}/*final_results.tab") , emit: tab
tuple val(meta), path("${prefix}/images/") , emit: images
tuple val(meta), path("${prefix}/logs/") , emit: logs
tuple val(meta), path("${prefix}/data/") , emit: data
tuple val(meta), path("${prefix}/database/") , emit: database
tuple val(meta), path("${prefix}/fasta_files/") , emit: fasta_files
tuple val(meta), path("${prefix}/kmer/") , emit: kmer
path "versions.yml" , emit: version
script:
def software = getSoftwareName(task.process)
prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
"""
plasmidID \\
-d $fasta \\
-s $prefix \\
-c $scaffold \\
$options.args \\
-o .
mv NO_GROUP/$prefix ./$prefix
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(plasmidID --version 2>&1)
END_VERSIONS
"""
}