mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-20 23:32:05 +00:00
c1eb9cce44
* Trimmomatic main only first draft * Add test files * SE PE Adjustment * Remove extra reads input * chore: Remove TODOs * Apply suggestions from code review Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com> * fix(trimmomatic): Handle SE output correctly Since there's never going to be unpaired reads for SE reads we can get away with it for SE * fix(trimmomatic): Use correct elvis operator to handle logic * fix(trimmomatic): Add hack to work with SE and PE reads * Update test.yml * use the PE and SE trimming correctly * Made user set adaptors * Add documentation * test(trimmomatic): Add files to pytest_modules * test(trimmomatic): Update name of failing test Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com> Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>
46 lines
1.6 KiB
Text
46 lines
1.6 KiB
Text
process TRIMMOMATIC {
|
|
tag "$meta.id"
|
|
label 'process_medium'
|
|
|
|
conda (params.enable_conda ? "bioconda::trimmomatic=0.39" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/trimmomatic:0.39--hdfd78af_2':
|
|
'quay.io/biocontainers/trimmomatic:0.39--hdfd78af_2' }"
|
|
|
|
input:
|
|
tuple val(meta), path(reads)
|
|
|
|
output:
|
|
tuple val(meta), path("*.paired.trim*.fastq.gz") , emit: trimmed_reads
|
|
tuple val(meta), path("*.unpaired.trim_*.fastq.gz"), optional:true, emit: unpaired_reads
|
|
tuple val(meta), path("*.log") , emit: log
|
|
path "versions.yml" , emit: versions
|
|
|
|
when:
|
|
task.ext.when == null || task.ext.when
|
|
|
|
script:
|
|
def args = task.ext.args ?: ''
|
|
def prefix = task.ext.prefix ?: "${meta.id}"
|
|
def trimmed = meta.single_end ? "SE" : "PE"
|
|
def output = meta.single_end ?
|
|
"${prefix}.SE.paired.trim.fastq.gz" // HACK to avoid unpaired and paired in the trimmed_reads output
|
|
: "${prefix}.paired.trim_1.fastq.gz ${prefix}.unpaired.trim_1.fastq.gz ${prefix}.paired.trim_2.fastq.gz ${prefix}.unpaired.trim_2.fastq.gz"
|
|
// TODO Give better error output
|
|
def qual_trim = task.ext.args2 ?: ''
|
|
"""
|
|
trimmomatic \\
|
|
$trimmed \\
|
|
-threads $task.cpus \\
|
|
-trimlog ${prefix}.log \\
|
|
$reads \\
|
|
$output \\
|
|
$qual_trim \\
|
|
$args
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
trimmomatic: \$(trimmomatic -version)
|
|
END_VERSIONS
|
|
"""
|
|
}
|