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https://github.com/MillironX/nf-core_modules.git
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f32dc15414
* update bclconvert module, as used in nf-core/demultiplex * reconfigure test with new test data * update test * formatting * update outputs, update meta * update module and test * update test config, test.yml * fix linting * emit logs and reports as dir * fix typo, recreate test.yml * fix linting Co-authored-by: CMGG ICT Team <ict@cmgg.be>
42 lines
1.5 KiB
Text
42 lines
1.5 KiB
Text
process BCLCONVERT {
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tag "$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 bcl-convert. Please use docker or singularity containers."
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}
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container "nfcore/bclconvert:3.9.3"
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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") ,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("Logs") ,emit: logs
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tuple val(meta), path("**.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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bcl-convert \\
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$args \\
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--output-directory . \\
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--bcl-input-directory ${run_dir} \\
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--sample-sheet ${samplesheet} \\
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--bcl-num-parallel-tiles ${task.cpus}
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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bclconvert: \$(bcl-convert -V 2>&1 | head -n 1 | sed 's/^.*Version //')
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END_VERSIONS
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"""
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}
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