nf-core_modules/modules/pirate/main.nf
Robert A. Petit III 053797510d
add pirate module (#777)
* new module pirate

* remove md5 check for non reproducible binary files

* get those to-dos out

* Update main.nf

* Update meta.yml

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 22:28:25 +01:00

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
params.options = [:]
options = initOptions(params.options)
process PIRATE {
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::pirate=1.0.4" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/pirate%3A1.0.4--hdfd78af_1"
} else {
container "quay.io/biocontainers/pirate:1.0.4--hdfd78af_1"
}
input:
tuple val(meta), path(gff)
output:
tuple val(meta), path("results/*") , emit: results
tuple val(meta), path("results/core_alignment.fasta"), optional: true, emit: aln
path "versions.yml" , emit: versions
script:
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
"""
PIRATE \\
$options.args \\
--threads $task.cpus \\
--input ./ \\
--output results/
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$( echo \$( PIRATE --version 2>&1) | sed 's/PIRATE //' )
END_VERSIONS
"""
}