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refactor: use tool name 'bracken' only

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This commit is contained in:
Moritz E. Beber 2022-10-21 10:03:36 +02:00
parent 8deb7757d8
commit 385507ec6f
1 changed files with 6 additions and 10 deletions
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16
subworkflows/local/profiling.nf
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@ -41,7 +41,7 @@ workflow PROFILING {
.combine(databases) .combine(databases)
.branch { .branch {
malt: it[2]['tool'] == 'malt' malt: it[2]['tool'] == 'malt'
kraken2: it[2]['tool'].contains('kraken2') kraken2: it[2]['tool'] == 'kraken2' || it[2]['tool'] == 'bracken'
metaphlan3: it[2]['tool'] == 'metaphlan3' metaphlan3: it[2]['tool'] == 'metaphlan3'
centrifuge: it[2]['tool'] == 'centrifuge' centrifuge: it[2]['tool'] == 'centrifuge'
kaiju: it[2]['tool'] == 'kaiju' kaiju: it[2]['tool'] == 'kaiju'
@ -133,7 +133,7 @@ workflow PROFILING {
ch_raw_classifications = ch_raw_classifications.mix( KRAKEN2_KRAKEN2.out.classified_reads_assignment ) ch_raw_classifications = ch_raw_classifications.mix( KRAKEN2_KRAKEN2.out.classified_reads_assignment )
ch_raw_profiles = ch_raw_profiles.mix( ch_raw_profiles = ch_raw_profiles.mix(
KRAKEN2_KRAKEN2.out.report KRAKEN2_KRAKEN2.out.report
// Set the tool to be strictly 'kraken2' instead of potentially 'kraken2+bracken' for downstream use. // Set the tool to be strictly 'kraken2' instead of potentially 'bracken' for downstream use.
.map { meta, report -> [meta + [tool: 'kraken2'], report]} .map { meta, report -> [meta + [tool: 'kraken2'], report]}
) )
@ -142,7 +142,7 @@ workflow PROFILING {
if ( params.run_kraken2 && params.run_bracken ) { if ( params.run_kraken2 && params.run_bracken ) {
def ch_input_for_bracken = KRAKEN2_KRAKEN2.out.report def ch_input_for_bracken = KRAKEN2_KRAKEN2.out.report
.filter { meta, report -> meta['tool'].contains('bracken') } .filter { meta, report -> meta['tool'] == 'bracken' }
if (params.kraken2_save_minimizers) { if (params.kraken2_save_minimizers) {
ch_input_for_bracken = KRAKEN2_STANDARD_REPORT(ch_input_for_bracken).report ch_input_for_bracken = KRAKEN2_STANDARD_REPORT(ch_input_for_bracken).report
@ -151,21 +151,17 @@ workflow PROFILING {
ch_input_for_bracken = ch_input_for_bracken ch_input_for_bracken = ch_input_for_bracken
.combine( .combine(
databases.filter { meta, db -> databases.filter { meta, db ->
meta['tool'].contains('bracken') meta['tool'] == 'bracken'
} }
) )
.multiMap { meta, report, db_meta, db -> .multiMap { meta, report, db_meta, db ->
report: [meta, report] report: [meta + db_meta, report]
db: db db: db
} }
BRACKEN_BRACKEN(ch_input_for_bracken.report, ch_input_for_bracken.db) BRACKEN_BRACKEN(ch_input_for_bracken.report, ch_input_for_bracken.db)
ch_versions = ch_versions.mix(BRACKEN_BRACKEN.out.versions.first()) ch_versions = ch_versions.mix(BRACKEN_BRACKEN.out.versions.first())
ch_raw_profiles = ch_raw_profiles.mix( ch_raw_profiles = ch_raw_profiles.mix(BRACKEN_BRACKEN.out.reports)
BRACKEN_BRACKEN.out.reports
// Set the tool to be strictly 'bracken' instead of potentially 'kraken2+bracken' for downstream use.
.map { meta, report -> [meta + [tool: 'bracken'], report]}
)
} }