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feat: introduce sample batches for krakenuniq

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Moritz E. Beber 2023-03-30 16:49:22 +02:00
parent b299a25bc7
commit 70dd7cade9
2 changed files with 15 additions and 10 deletions
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1
nextflow.config
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@ -125,6 +125,7 @@ params {
krakenuniq_ram_chunk_size = '16G' krakenuniq_ram_chunk_size = '16G'
krakenuniq_save_reads = false // added directly to module in profiling.nf krakenuniq_save_reads = false // added directly to module in profiling.nf
krakenuniq_save_readclassifications = false // added directly to module in profiling.nf krakenuniq_save_readclassifications = false // added directly to module in profiling.nf
krakenuniq_batch_size = 20
// Bracken // Bracken
run_bracken = false run_bracken = false

24
subworkflows/local/profiling.nf
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@ -315,16 +315,20 @@ workflow PROFILING {
if ( params.run_krakenuniq ) { if ( params.run_krakenuniq ) {
ch_input_for_krakenuniq = ch_input_for_profiling.krakenuniq ch_input_for_krakenuniq = ch_input_for_profiling.krakenuniq
.map { .map {
meta, reads, db_meta, db -> meta, reads, db_meta, db ->
[[id: db_meta.db_name, single_end: meta.single_end], reads, db_meta, db] [[id: db_meta.db_name, single_end: meta.single_end], reads, db_meta, db]
} }
.groupTuple(by: [0,2,3]) .groupTuple(by: [0,2,3])
.multiMap { .flatMap { single_meta, reads, db_meta, db ->
single_meta, reads, db_meta, db -> def batches = reads.collate(params.krakenuniq_batch_size)
reads: [ single_meta + db_meta, reads.flatten() ] return batches.colect { batch -> [ single_meta + db_meta, batch.flatten(), db ]}
db: db }
} .multiMap {
meta, reads, db ->
reads: [ meta, reads ]
db: db
}
// Hardcode to _always_ produce the report file (which is our basic output, and goes into) // Hardcode to _always_ produce the report file (which is our basic output, and goes into)
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 ) 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 )
ch_multiqc_files = ch_multiqc_files.mix( KRAKENUNIQ_PRELOADEDKRAKENUNIQ.out.report ) ch_multiqc_files = ch_multiqc_files.mix( KRAKENUNIQ_PRELOADEDKRAKENUNIQ.out.report )