nf-core_modules/modules/cellranger/mkfastq/main.nf

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process CELLRANGER_MKFASTQ {
tag "mkfastq"
label 'process_medium'
if (params.enable_conda) {
exit 1, "Conda environments cannot be used when using the Cell Ranger tool. Please use docker or singularity containers."
}
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container "nfcore/cellrangermkfastq:7.0.0"
input:
path bcl
path csv
output:
path "versions.yml", emit: versions
path "${bcl.getSimpleName()}/outs/fastq_path/*.fastq.gz" , emit: fastq
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when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
"""
cellranger mkfastq --id=${bcl.getSimpleName()} \
--run=$bcl \
--csv=$csv \
$args
cat <<-END_VERSIONS > versions.yml
"${task.process}":
cellranger: \$(echo \$( cellranger --version 2>&1) | sed 's/^.*[^0-9]\\([0-9]*\\.[0-9]*\\.[0-9]*\\).*\$/\\1/' )
END_VERSIONS
"""
stub:
"""
mkdir -p "${bcl.getSimpleName()}/outs/fastq_path/"
touch ${bcl.getSimpleName()}/outs/fastq_path/fake_file.fastq.gz
cat <<-END_VERSIONS > versions.yml
"${task.process}":
cellranger: \$(echo \$( cellranger --version 2>&1) | sed 's/^.*[^0-9]\\([0-9]*\\.[0-9]*\\.[0-9]*\\).*\$/\\1/' )
END_VERSIONS
"""
}