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refactor: rename process to kraken2
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parent
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commit
563b34c9c3
2 changed files with 3 additions and 3 deletions
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@ -1,4 +1,4 @@
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process KRAKEN_STANDARD_REPORT {
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process KRAKEN2_STANDARD_REPORT {
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tag "$meta.id"
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tag "$meta.id"
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label 'process_single'
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label 'process_single'
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@ -5,7 +5,7 @@
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include { MALT_RUN } from '../../modules/nf-core/malt/run/main'
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include { MALT_RUN } from '../../modules/nf-core/malt/run/main'
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include { MEGAN_RMA2INFO as MEGAN_RMA2INFO_TSV } from '../../modules/nf-core/megan/rma2info/main'
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include { MEGAN_RMA2INFO as MEGAN_RMA2INFO_TSV } from '../../modules/nf-core/megan/rma2info/main'
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include { KRAKEN2_KRAKEN2 } from '../../modules/nf-core/kraken2/kraken2/main'
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include { KRAKEN2_KRAKEN2 } from '../../modules/nf-core/kraken2/kraken2/main'
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include { KRAKEN_STANDARD_REPORT } from '../../modules/local/kraken_standard_report'
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include { KRAKEN2_STANDARD_REPORT } from '../../modules/local/kraken2_standard_report'
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include { BRACKEN_BRACKEN } from '../../modules/nf-core/bracken/bracken/main'
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include { BRACKEN_BRACKEN } from '../../modules/nf-core/bracken/bracken/main'
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include { CENTRIFUGE_CENTRIFUGE } from '../../modules/nf-core/centrifuge/centrifuge/main'
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include { CENTRIFUGE_CENTRIFUGE } from '../../modules/nf-core/centrifuge/centrifuge/main'
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include { CENTRIFUGE_KREPORT } from '../../modules/nf-core/centrifuge/kreport/main'
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include { CENTRIFUGE_KREPORT } from '../../modules/nf-core/centrifuge/kreport/main'
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@ -140,7 +140,7 @@ workflow PROFILING {
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def ch_input_for_bracken
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def ch_input_for_bracken
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if (params.kraken2_save_minimizers) {
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if (params.kraken2_save_minimizers) {
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ch_input_for_bracken = KRAKEN_STANDARD_REPORT(KRAKEN2_KRAKEN2.out.report).report
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ch_input_for_bracken = KRAKEN2_STANDARD_REPORT(KRAKEN2_KRAKEN2.out.report).report
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} else {
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} else {
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ch_input_for_bracken = KRAKEN2_KRAKEN2.out.report
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ch_input_for_bracken = KRAKEN2_KRAKEN2.out.report
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}
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}
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