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Update output paths in bases2fastq module #9436

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Update output paths in bases2fastq module #9436

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22 changes: 12 additions & 10 deletions modules/nf-core/bases2fastq/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -8,15 +8,15 @@ process BASES2FASTQ {
tuple val(meta), path(run_manifest), path(run_dir)

output:
tuple val(meta), path('output/Samples/**/*_R*.fastq.gz'), emit: sample_fastq
tuple val(meta), path('output/Samples/**/*_stats.json') , emit: sample_json
tuple val(meta), path('output/*_QC.html') , emit: qc_report
tuple val(meta), path('output/multiqc_report.html') , emit: multiqc_report, optional: true
tuple val(meta), path('output/RunStats.json') , emit: run_stats
tuple val(meta), path('output/RunManifest.json') , emit: generated_run_manifest
tuple val(meta), path('output/Metrics.csv') , emit: metrics
tuple val(meta), path('output/UnassignedSequences.csv') , emit: unassigned
path "versions.yml" , emit: versions
tuple val(meta), path('*/Samples/**/*_R*.fastq.gz'), emit: sample_fastq
tuple val(meta), path('*/Samples/**/*_stats.json') , emit: sample_json
tuple val(meta), path('*/*_QC.html') , emit: qc_report
tuple val(meta), path('*/multiqc_report.html') , emit: multiqc_report, optional: true
tuple val(meta), path('*/RunStats.json') , emit: run_stats
tuple val(meta), path('*/RunManifest.json') , emit: generated_run_manifest
tuple val(meta), path('*/Metrics.csv') , emit: metrics
tuple val(meta), path('*/UnassignedSequences.csv') , emit: unassigned
path "versions.yml" , emit: versions

when:
task.ext.when == null || task.ext.when
Expand All @@ -28,13 +28,15 @@ process BASES2FASTQ {
}
def args = task.ext.args ?: ''
def runManifest = run_manifest ? "-r ${run_manifest}" : ""
def prefix = task.ext.prefix ?: "${meta.id}"

"""
bases2fastq \\
-p $task.cpus \\
$runManifest \\
$args \\
$run_dir \\
output
$prefix

cat <<-END_VERSIONS > versions.yml
"${task.process}":
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