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

🐛 FIX: remove suffix option (#1188)

Browse source
This commit is contained in:
Sébastien Guizard 2021-12-24 11:32:30 +00:00 committed by GitHub
parent cde237e7ce
commit c0e1489133
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
1 changed files with 8 additions and 3 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

11
modules/lima/main.nf
View file

@ -12,9 +12,7 @@ process LIMA {
path primers
output:
tuple val(meta), path("*.clips") , emit: clips
tuple val(meta), path("*.counts") , emit: counts
tuple val(meta), path("*.guess") , emit: guess
tuple val(meta), path("*.report") , emit: report
tuple val(meta), path("*.summary"), emit: summary
path "versions.yml" , emit: versions
@ -27,10 +25,18 @@ process LIMA {
tuple val(meta), path("*.fastq.gz") , optional: true, emit: fastqgz
tuple val(meta), path("*.xml") , optional: true, emit: xml
tuple val(meta), path("*.json") , optional: true, emit: json
tuple val(meta), path("*.clips") , optional: true, emit: clips
tuple val(meta), path("*.guess") , optional: true, emit: guess
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
if( "$ccs" == "${prefix}.bam" ) error "Input and output names are the same, set prefix in module configuration"
if( "$ccs" == "${prefix}.fasta" ) error "Input and output names are the same, set prefix in module configuration"
if( "$ccs" == "${prefix}.fasta.gz" ) error "Input and output names are the same, set prefix in module configuration"
if( "$ccs" == "${prefix}.fastq" ) error "Input and output names are the same, set prefix in module configuration"
if( "$ccs" == "${prefix}.fastq.gz" ) error "Input and output names are the same, set prefix in module configuration"
"""
OUT_EXT=""
@ -46,7 +52,6 @@ process LIMA {
OUT_EXT="fastq.gz"
fi
echo \$OUT_EXT
lima \\
$ccs \\
$primers \\