mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-15 06:03:10 +00:00
15fd90ffe8
* initial stubs [ci skip] * remove comments and add main command [ci skip] * design iteration [ci skip] * add new standard functions.nf [ci skip] * update the version string [ci skip] * accomodate the db stubs and single/double ends [ci skip] * add FIXME for missing info [ci skip] * Accomodate the results folder [ci skip] * Update main.nf * Apply suggestions from code review * Update main.nf * Apply suggestions from code review * Add version file to stubs [ci skip] * Tweak the output dir pattern [ci skip] * Update modules/phyloflash/main.nf * Update modules/phyloflash/main.nf * Update modules/phyloflash/main.nf Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
85 lines
2.6 KiB
Text
85 lines
2.6 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
|
|
|
params.options = [:]
|
|
options = initOptions(params.options)
|
|
|
|
process PHYLOFLASH {
|
|
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::phyloflash=3.4" : null)
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
|
container "https://depot.galaxyproject.org/singularity/phyloflash:3.4--hdfd78af_1"
|
|
} else {
|
|
container "quay.io/biocontainers/phyloflash:3.4--hdfd78af_1"
|
|
}
|
|
|
|
input:
|
|
tuple val(meta), path(reads)
|
|
path silva_db
|
|
path univec_db
|
|
|
|
output:
|
|
tuple val(meta), path("${meta.id}*/*"), emit: results
|
|
path "versions.yml" , emit: versions
|
|
|
|
script:
|
|
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
|
|
|
if (meta.single_end) {
|
|
"""
|
|
phyloFlash.pl \\
|
|
$options.args \\
|
|
-read1 ${reads[0]} \\
|
|
-lib $prefix \\
|
|
-interleaved \\
|
|
-dbhome . \\
|
|
-CPUs $task.cpus
|
|
|
|
mkdir $prefix
|
|
mv ${prefix}.* $prefix
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
${getProcessName(task.process)}:
|
|
${getSoftwareName(task.process)}: \$(echo \$(phyloFlash.pl -version 2>&1) | sed "s/^.*phyloFlash v//")
|
|
END_VERSIONS
|
|
"""
|
|
} else {
|
|
"""
|
|
phyloFlash.pl \\
|
|
$options.args \\
|
|
-read1 ${reads[0]} \\
|
|
-read2 ${reads[1]} \\
|
|
-lib $prefix \\
|
|
-dbhome . \\
|
|
-CPUs $task.cpus
|
|
|
|
mkdir $prefix
|
|
mv ${prefix}.* $prefix
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
${getProcessName(task.process)}:
|
|
${getSoftwareName(task.process)}: \$(echo \$(phyloFlash.pl -version 2>&1) | sed "s/^.*phyloFlash v//")
|
|
END_VERSIONS
|
|
"""
|
|
}
|
|
|
|
stub:
|
|
|
|
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
|
|
|
"""
|
|
mkdir ${prefix}
|
|
touch ${prefix}/${prefix}.SSU.collection.fasta
|
|
touch ${prefix}/${prefix}.phyloFlash
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
${getProcessName(task.process)}:
|
|
${getSoftwareName(task.process)}: \$(echo \$(phyloFlash.pl -version 2>&1) | sed "s/^.*phyloFlash v//")
|
|
END_VERSIONS
|
|
"""
|
|
}
|