millironx/nf-core_modules
1
0
Fork 0
mirror of https://github.com/MillironX/nf-core_modules.git synced 2024-12-22 11:08:17 +00:00
Code Issues Releases Packages Activity

Actually add the changes

Browse source
This commit is contained in:
James Fellows Yates 2022-05-31 15:49:57 +02:00
parent edc9e83a7d
commit 089f761f0b
1 changed files with 3 additions and 2 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

5
modules/filtlong/main.nf
View file

@ -11,7 +11,7 @@ process FILTLONG {
tuple val(meta), path(shortreads), path(longreads)
output:
tuple val(meta), path("${meta.id}_lr_filtlong.fastq.gz"), emit: reads
tuple val(meta), path("*.fastq.gz"), emit: reads
path "versions.yml" , emit: versions
when:
@ -21,12 +21,13 @@ process FILTLONG {
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def short_reads = !shortreads ? "" : meta.single_end ? "-1 $shortreads" : "-1 ${shortreads[0]} -2 ${shortreads[1]}"
if ("$longreads" == "${prefix}.fastq.gz") error "Longread FASTQ input and output names are the same, set prefix in module configuration to disambiguate!"
"""
filtlong \\
$short_reads \\
$args \\
$longreads \\
| gzip -n > ${prefix}_lr_filtlong.fastq.gz
| gzip -n > ${prefix}.fastq.gz
cat <<-END_VERSIONS > versions.yml
"${task.process}":