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add missing parameters to nextflow.config
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2 changed files with 7 additions and 1 deletions
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@ -335,7 +335,8 @@ process {
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withName: KRAKENUNIQ_PRELOADEDKRAKENUNIQ {
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ext.args = { "${meta.db_params}" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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// one run with multiple samples, so fix ID to just db name to ensure clean log name
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ext.prefix = { "${meta.db_name}" }
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publishDir = [
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path: { "${params.outdir}/krakenuniq/${meta.db_name}/" },
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mode: params.publish_dir_mode,
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@ -118,6 +118,11 @@ params {
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kraken2_save_readclassification = false // added directly to module in profiling.nf
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kraken2_save_minimizers = false
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//krakenuniq
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run_krakenuniq = false
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krakenuniq_save_reads = false // added directly to module in profiling.nf
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krakenuniq_save_readclassifications = false // added directly to module in profiling.nf
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// Bracken
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run_bracken = false
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