|
|
|
@ -12,15 +12,14 @@ process ADAPTERREMOVAL {
|
|
|
|
|
path(adapterlist)
|
|
|
|
|
|
|
|
|
|
output:
|
|
|
|
|
tuple val(meta), path("${prefix}.truncated.gz") , optional: true, emit: singles_truncated
|
|
|
|
|
tuple val(meta), path("${prefix}.discarded.gz") , optional: true, emit: discarded
|
|
|
|
|
tuple val(meta), path("${prefix}.pair1.truncated.gz") , optional: true, emit: pair1_truncated
|
|
|
|
|
tuple val(meta), path("${prefix}.pair2.truncated.gz") , optional: true, emit: pair2_truncated
|
|
|
|
|
tuple val(meta), path("${prefix}.collapsed.gz") , optional: true, emit: collapsed
|
|
|
|
|
tuple val(meta), path("${prefix}.collapsed.truncated.gz") , optional: true, emit: collapsed_truncated
|
|
|
|
|
tuple val(meta), path("${prefix}.paired.gz") , optional: true, emit: paired_interleaved
|
|
|
|
|
tuple val(meta), path('*.log') , emit: log
|
|
|
|
|
path "versions.yml" , emit: versions
|
|
|
|
|
tuple val(meta), path("${prefix}.truncated.fastq.gz") , optional: true, emit: singles_truncated
|
|
|
|
|
tuple val(meta), path("${prefix}.discarded.fastq.gz") , optional: true, emit: discarded
|
|
|
|
|
tuple val(meta), path("${prefix}.pair{1,2}.truncated.fastq.gz") , optional: true, emit: paired_truncated
|
|
|
|
|
tuple val(meta), path("${prefix}.collapsed.fastq.gz") , optional: true, emit: collapsed
|
|
|
|
|
tuple val(meta), path("${prefix}.collapsed.truncated.fastq.gz") , optional: true, emit: collapsed_truncated
|
|
|
|
|
tuple val(meta), path("${prefix}.paired.fastq.gz") , optional: true, emit: paired_interleaved
|
|
|
|
|
tuple val(meta), path('*.settings') , emit: settings
|
|
|
|
|
path "versions.yml" , emit: versions
|
|
|
|
|
|
|
|
|
|
when:
|
|
|
|
|
task.ext.when == null || task.ext.when
|
|
|
|
@ -38,10 +37,19 @@ process ADAPTERREMOVAL {
|
|
|
|
|
$adapterlist \\
|
|
|
|
|
--basename ${prefix} \\
|
|
|
|
|
--threads ${task.cpus} \\
|
|
|
|
|
--settings ${prefix}.log \\
|
|
|
|
|
--seed 42 \\
|
|
|
|
|
--gzip
|
|
|
|
|
|
|
|
|
|
ensure_fastq() {
|
|
|
|
|
if [ -f "\${1}" ]; then
|
|
|
|
|
mv "\${1}" "\${1::-3}.fastq.gz"
|
|
|
|
|
fi
|
|
|
|
|
|
|
|
|
|
}
|
|
|
|
|
|
|
|
|
|
ensure_fastq '${prefix}.truncated.gz'
|
|
|
|
|
ensure_fastq '${prefix}.discarded.gz'
|
|
|
|
|
|
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
|
|
|
"${task.process}":
|
|
|
|
|
adapterremoval: \$(AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g")
|
|
|
|
@ -56,10 +64,24 @@ process ADAPTERREMOVAL {
|
|
|
|
|
$adapterlist \\
|
|
|
|
|
--basename ${prefix} \\
|
|
|
|
|
--threads $task.cpus \\
|
|
|
|
|
--settings ${prefix}.log \\
|
|
|
|
|
--seed 42 \\
|
|
|
|
|
--gzip
|
|
|
|
|
|
|
|
|
|
ensure_fastq() {
|
|
|
|
|
if [ -f "\${1}" ]; then
|
|
|
|
|
mv "\${1}" "\${1::-3}.fastq.gz"
|
|
|
|
|
fi
|
|
|
|
|
|
|
|
|
|
}
|
|
|
|
|
|
|
|
|
|
ensure_fastq '${prefix}.truncated.gz'
|
|
|
|
|
ensure_fastq '${prefix}.discarded.gz'
|
|
|
|
|
ensure_fastq '${prefix}.pair1.truncated.gz'
|
|
|
|
|
ensure_fastq '${prefix}.pair2.truncated.gz'
|
|
|
|
|
ensure_fastq '${prefix}.collapsed.gz'
|
|
|
|
|
ensure_fastq '${prefix}.collapsed.truncated.gz'
|
|
|
|
|
ensure_fastq '${prefix}.paired.gz'
|
|
|
|
|
|
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
|
|
|
"${task.process}":
|
|
|
|
|
adapterremoval: \$(AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g")
|
|
|
|
|