nf-core_modules/software/adapterremoval/main.nf
Maxime Borry aa76c6d870
new module: AdapterRemoval (#309)
* add adapterremoval module

* fix indentations

* switch to process_medium

* update docker tests

* remove duplicated entry

* fix line ending

* Update software/adapterremoval/main.nf

* Update software/adapterremoval/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-22 17:16:04 +00:00

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2.7 KiB
Text

include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
process ADAPTERREMOVAL {
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), publish_id:meta.id) }
conda (params.enable_conda ? "bioconda::adapterremoval=2.3.2" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/adapterremoval:2.3.2--hb7ba0dd_0"
} else {
container "quay.io/biocontainers/adapterremoval:2.3.2--hb7ba0dd_0"
}
input:
tuple val(meta), path(reads)
output:
tuple val(meta), path('*.fastq.gz'), emit: reads
tuple val(meta), path('*.log') , emit: log
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
if (meta.single_end) {
"""
AdapterRemoval \\
--file1 $reads \\
$options.args \\
--basename $prefix \\
--threads $task.cpus \\
--settings ${prefix}.log \\
--output1 ${prefix}.trimmed.fastq.gz \\
--seed 42 \\
--gzip \\
AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g" > ${software}.version.txt
"""
} else if (!meta.single_end && !meta.collapse) {
"""
AdapterRemoval \\
--file1 ${reads[0]} \\
--file2 ${reads[0]} \\
$options.args \\
--basename $prefix \\
--threads $task.cpus \\
--settings ${prefix}.log \\
--output1 ${prefix}.pair1.trimmed.fastq.gz \\
--output2 ${prefix}.pair2.trimmed.fastq.gz \\
--seed 42 \\
--gzip \\
AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g" > ${software}.version.txt
"""
} else {
"""
AdapterRemoval \\
--file1 ${reads[0]} \\
--file2 ${reads[0]} \\
--collapse \\
$options.args \\
--basename $prefix \\
--threads $task.cpus \\
--settings ${prefix}.log \\
--seed 42 \\
--gzip \\
cat *.collapsed.gz *.collapsed.truncated.gz > ${prefix}.merged.fastq.gz
AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g" > ${software}.version.txt
"""
}
}