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refactor: only combine same database name

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[skip ci]
This commit is contained in:
Moritz E. Beber 2022-10-27 11:19:14 +02:00
parent 0de1ac5356
commit dd1a4ff158
1 changed files with 14 additions and 11 deletions
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25
subworkflows/local/profiling.nf
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@ -141,22 +141,25 @@ workflow PROFILING {
}
if ( params.run_kraken2 && params.run_bracken ) {
// remove files from 'pure' kraken2 runs, so only those aligned against bracken2 kraken database are taken for brakcen
def ch_input_for_bracken = KRAKEN2_KRAKEN2.out.report
// Remove files from 'pure' kraken2 runs, so only those aligned against Bracken & kraken2 database are used.
def ch_kraken2_output = KRAKEN2_KRAKEN2.out.report
.filter { meta, report -> meta['tool'] == 'bracken' }
// If necessary, convert the eight column output to six column output.
if (params.kraken2_save_minimizers) {
ch_input_for_bracken = KRAKEN2_STANDARD_REPORT(ch_input_for_bracken).report
ch_kraken2_output = KRAKEN2_STANDARD_REPORT(ch_kraken2_output).report
}
ch_input_for_bracken = ch_input_for_bracken
.combine(
databases.filter { meta, db ->
meta['tool'] == 'bracken'
}
)
.multiMap { meta, report, db_meta, db ->
// Extract the database name to combine by.
def ch_bracken_databases = databases
.filter { meta, db -> meta['tool'] == 'bracken' }
.map { meta, db -> [meta['db_name'], meta, db] }
// Extract the database name to combine by.
def ch_input_for_bracken = ch_kraken2_output
.map { meta, report -> [meta['db_name'], meta, report] }
.combine(ch_bracken_databases, by: 0)
.multiMap { key, meta, report, db_meta, db ->
report: [meta + db_meta, report]
db: db
}