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43 lines
1.6 KiB
Text
43 lines
1.6 KiB
Text
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process BCL2FASTQ {
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tag {"$meta.lane" ? "$meta.id"+"."+"$meta.lane" : "$meta.id" }
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label 'process_high'
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if (params.enable_conda) {
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exit 1, "Conda environments cannot be used when using bcl2fastq. Please use docker or singularity containers."
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}
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container "nfcore/bcl2fastq:2.20.0.422"
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input:
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tuple val(meta), path(samplesheet), path(run_dir)
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output:
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tuple val(meta), path("**[!Undetermined]_S*_L00?_R?_00?.fastq.gz") ,emit: fastq
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tuple val(meta), path("**_S*_L00?_I?_00?.fastq.gz") ,optional:true ,emit: fastq_idx
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tuple val(meta), path("Undetermined_S0_L00?_R?_00?.fastq.gz") ,optional:true ,emit: undetermined
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tuple val(meta), path("Undetermined_S0_L00?_I?_00?.fastq.gz") ,optional:true, emit: undetermined_idx
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tuple val(meta), path("Reports") ,emit: reports
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tuple val(meta), path("Stats") ,emit: stats
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tuple val(meta), path("**/InterOp/*.bin") ,emit: interop
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path("versions.yml") ,emit: versions
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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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bcl2fastq \\
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$args \\
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--output-dir . \\
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--runfolder-dir ${run_dir} \\
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--sample-sheet ${samplesheet} \\
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--processing-threads ${task.cpus}
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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bcl2fastq: \$(bcl2fastq -V 2>&1 | grep -m 1 bcl2fastq | sed 's/^.*bcl2fastq v//')
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END_VERSIONS
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"""
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}
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