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feat: introduce sample batches for krakenuniq
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commit
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2 changed files with 15 additions and 10 deletions
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@ -125,6 +125,7 @@ params {
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krakenuniq_ram_chunk_size = '16G'
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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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krakenuniq_batch_size = 20
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// Bracken
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run_bracken = false
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@ -315,16 +315,20 @@ workflow PROFILING {
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if ( params.run_krakenuniq ) {
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ch_input_for_krakenuniq = ch_input_for_profiling.krakenuniq
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.map {
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meta, reads, db_meta, db ->
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[[id: db_meta.db_name, single_end: meta.single_end], reads, db_meta, db]
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}
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.groupTuple(by: [0,2,3])
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.multiMap {
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single_meta, reads, db_meta, db ->
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reads: [ single_meta + db_meta, reads.flatten() ]
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db: db
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}
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.map {
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meta, reads, db_meta, db ->
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[[id: db_meta.db_name, single_end: meta.single_end], reads, db_meta, db]
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}
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.groupTuple(by: [0,2,3])
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.flatMap { single_meta, reads, db_meta, db ->
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def batches = reads.collate(params.krakenuniq_batch_size)
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return batches.colect { batch -> [ single_meta + db_meta, batch.flatten(), db ]}
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}
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.multiMap {
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meta, reads, db ->
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reads: [ meta, reads ]
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db: db
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}
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// Hardcode to _always_ produce the report file (which is our basic output, and goes into)
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KRAKENUNIQ_PRELOADEDKRAKENUNIQ ( ch_input_for_krakenuniq.reads, ch_input_for_krakenuniq.db, params.krakenuniq_ram_chunk_size, params.krakenuniq_save_reads, true, params.krakenuniq_save_readclassifications )
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ch_multiqc_files = ch_multiqc_files.mix( KRAKENUNIQ_PRELOADEDKRAKENUNIQ.out.report )
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