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45 lines
1.2 KiB
Text
45 lines
1.2 KiB
Text
process CELLRANGER_MKFASTQ {
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tag "mkfastq"
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label 'process_medium'
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if (params.enable_conda) {
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exit 1, "Conda environments cannot be used when using the Cell Ranger tool. Please use docker or singularity containers."
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}
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container "nfcore/cellrangermkfastq:6.1.2"
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input:
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path bcl
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path csv
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output:
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path "versions.yml", emit: versions
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path "${bcl.getSimpleName()}/outs/fastq_path/*.fastq.gz" , emit: fastq
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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"""
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cellranger mkfastq --id=${bcl.getSimpleName()} \
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--run=$bcl \
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--csv=$csv \
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$args
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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cellranger: \$(echo \$( cellranger --version 2>&1) | sed 's/^.*[^0-9]\\([0-9]*\\.[0-9]*\\.[0-9]*\\).*\$/\\1/' )
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END_VERSIONS
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"""
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stub:
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"""
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mkdir -p "${bcl.getSimpleName()}/outs/fastq_path/"
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touch ${bcl.getSimpleName()}/outs/fastq_path/fake_file.fastq.gz
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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cellranger: \$(echo \$( cellranger --version 2>&1) | sed 's/^.*[^0-9]\\([0-9]*\\.[0-9]*\\.[0-9]*\\).*\$/\\1/' )
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END_VERSIONS
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"""
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}
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