mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 13:43:09 +00:00
9294259eea
* add bcl2fastq * test fixes * fixed tests * add tests to workflow * change container source
42 lines
1.6 KiB
Text
42 lines
1.6 KiB
Text
process BCL2FASTQ {
|
|
tag {"$meta.lane" ? "$meta.id"+"."+"$meta.lane" : "$meta.id" }
|
|
label 'process_high'
|
|
|
|
if (params.enable_conda) {
|
|
exit 1, "Conda environments cannot be used when using bcl2fastq. Please use docker or singularity containers."
|
|
}
|
|
container "nfcore/bcl2fastq:2.20.0.422"
|
|
|
|
input:
|
|
tuple val(meta), path(samplesheet), path(run_dir)
|
|
|
|
output:
|
|
tuple val(meta), path("**[!Undetermined]_S*_L00?_R?_00?.fastq.gz") ,emit: fastq
|
|
tuple val(meta), path("**_S*_L00?_I?_00?.fastq.gz") ,optional:true ,emit: fastq_idx
|
|
tuple val(meta), path("Undetermined_S0_L00?_R?_00?.fastq.gz") ,optional:true ,emit: undetermined
|
|
tuple val(meta), path("Undetermined_S0_L00?_I?_00?.fastq.gz") ,optional:true, emit: undetermined_idx
|
|
tuple val(meta), path("Reports") ,emit: reports
|
|
tuple val(meta), path("Stats") ,emit: stats
|
|
tuple val(meta), path("**/InterOp/*.bin") ,emit: interop
|
|
path("versions.yml") ,emit: versions
|
|
|
|
when:
|
|
task.ext.when == null || task.ext.when
|
|
|
|
script:
|
|
def args = task.ext.args ?: ''
|
|
|
|
"""
|
|
bcl2fastq \\
|
|
$args \\
|
|
--output-dir . \\
|
|
--runfolder-dir ${run_dir} \\
|
|
--sample-sheet ${samplesheet} \\
|
|
--processing-threads ${task.cpus}
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
bcl2fastq: \$(bcl2fastq -V 2>&1 | grep -m 1 bcl2fastq | sed 's/^.*bcl2fastq v//')
|
|
END_VERSIONS
|
|
"""
|
|
}
|