nf-core_modules/modules/bclconvert/main.nf

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process BCLCONVERT {
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 bcl-convert. Please use docker or singularity containers."
}
container "nfcore/bclconvert:4.0.3"
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
2022-06-24 05:14:42 +00:00
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("Logs") ,emit: logs
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 ?: ''
"""
bcl-convert \\
$args \\
--output-directory . \\
--bcl-input-directory ${run_dir} \\
--sample-sheet ${samplesheet} \\
--bcl-num-parallel-tiles ${task.cpus}
cat <<-END_VERSIONS > versions.yml
"${task.process}":
bclconvert: \$(bcl-convert -V 2>&1 | head -n 1 | sed 's/^.*Version //')
END_VERSIONS
"""
}