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refactor: rename process to kraken2

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This commit is contained in:
Moritz E. Beber 2022-10-14 14:48:27 +02:00
parent 95621ebd8a
commit 563b34c9c3
2 changed files with 3 additions and 3 deletions
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2
modules/local/kraken_standard_report.nf → modules/local/kraken2_standard_report.nf
View file

@ -1,4 +1,4 @@
process KRAKEN_STANDARD_REPORT { process KRAKEN2_STANDARD_REPORT {
tag "$meta.id" tag "$meta.id"
label 'process_single' label 'process_single'

4
subworkflows/local/profiling.nf
View file

@ -5,7 +5,7 @@
include { MALT_RUN } from '../../modules/nf-core/malt/run/main' include { MALT_RUN } from '../../modules/nf-core/malt/run/main'
include { MEGAN_RMA2INFO as MEGAN_RMA2INFO_TSV } from '../../modules/nf-core/megan/rma2info/main' include { MEGAN_RMA2INFO as MEGAN_RMA2INFO_TSV } from '../../modules/nf-core/megan/rma2info/main'
include { KRAKEN2_KRAKEN2 } from '../../modules/nf-core/kraken2/kraken2/main' include { KRAKEN2_KRAKEN2 } from '../../modules/nf-core/kraken2/kraken2/main'
include { KRAKEN_STANDARD_REPORT } from '../../modules/local/kraken_standard_report' include { KRAKEN2_STANDARD_REPORT } from '../../modules/local/kraken2_standard_report'
include { BRACKEN_BRACKEN } from '../../modules/nf-core/bracken/bracken/main' include { BRACKEN_BRACKEN } from '../../modules/nf-core/bracken/bracken/main'
include { CENTRIFUGE_CENTRIFUGE } from '../../modules/nf-core/centrifuge/centrifuge/main' include { CENTRIFUGE_CENTRIFUGE } from '../../modules/nf-core/centrifuge/centrifuge/main'
include { CENTRIFUGE_KREPORT } from '../../modules/nf-core/centrifuge/kreport/main' include { CENTRIFUGE_KREPORT } from '../../modules/nf-core/centrifuge/kreport/main'
@ -140,7 +140,7 @@ workflow PROFILING {
def ch_input_for_bracken def ch_input_for_bracken
if (params.kraken2_save_minimizers) { if (params.kraken2_save_minimizers) {
ch_input_for_bracken = KRAKEN_STANDARD_REPORT(KRAKEN2_KRAKEN2.out.report).report ch_input_for_bracken = KRAKEN2_STANDARD_REPORT(KRAKEN2_KRAKEN2.out.report).report
} else { } else {
ch_input_for_bracken = KRAKEN2_KRAKEN2.out.report ch_input_for_bracken = KRAKEN2_KRAKEN2.out.report
} }