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46 lines
1.5 KiB
Plaintext
46 lines
1.5 KiB
Plaintext
process BASES2FASTQ {
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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 bases2fastq. Please use docker or singularity containers."
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}
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container "elembio/bases2fastq:1.1.0"
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input:
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tuple val(meta), path(run_manifest), path(run_dir)
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output:
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tuple val(meta), path('output/Samples/*/*_R*.fastq.gz'), emit: sample_fastq
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tuple val(meta), path('output/Samples/*/*.json') , emit: sample_json
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tuple val(meta), path('output/*.html') , emit: qc_report
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tuple val(meta), path('output/RunStats.json') , emit: run_stats
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tuple val(meta), path('output/RunManifest.json') , emit: generated_run_manifest
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tuple val(meta), path('output/Metrics.csv') , emit: metrics
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tuple val(meta), path('output/UnassignedSequences.csv'), emit: unassigned
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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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def prefix = task.ext.prefix ?: "${meta.id}"
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def runManifest = run_manifest ? "-r ${run_manifest}" : ""
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"""
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ls
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bases2fastq \\
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-p $task.cpus \\
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$runManifest \\
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$args \\
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$run_dir \\
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output
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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bases2fastq: \$(bases2fastq --version | sed -e "s/bases2fastq version //g")
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END_VERSIONS
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"""
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}
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