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https://github.com/MillironX/taxprofiler.git
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Fix ugly warn when KAIJU2TABLE not run
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parent
f0f89eb082
commit
a5138ed6e0
3 changed files with 20 additions and 20 deletions
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@ -486,7 +486,7 @@ process {
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ext.args = { "${meta.db_params}" }
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}
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withName: '.*PROFILING:KAIJU_KAIJU2TABLE' {
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withName: 'KAIJU_KAIJU2TABLE_SINGLE' {
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ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.kaijutable" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.kaijutable" }
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publishDir = [
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path: { "${params.outdir}/kaiju/${meta.db_name}/" },
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@ -495,7 +495,7 @@ process {
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]
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}
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withName: '.*STANDARDISATION_PROFILES:KAIJU_KAIJU2TABLE' {
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withName: 'KAIJU_KAIJU2TABLE_COMBINED' {
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ext.prefix = { "kaiju_${meta.id}_combined_reports" }
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publishDir = [
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path: { "${params.outdir}/kaiju/" },
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@ -2,19 +2,19 @@
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// Run profiling
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//
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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 { KRAKEN2_KRAKEN2 } from '../../modules/nf-core/kraken2/kraken2/main'
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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 { 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 { METAPHLAN3_METAPHLAN3 } from '../../modules/nf-core/metaphlan3/metaphlan3/main'
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include { KAIJU_KAIJU } from '../../modules/nf-core/kaiju/kaiju/main'
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include { KAIJU_KAIJU2TABLE } from '../../modules/nf-core/kaiju/kaiju2table/main'
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include { DIAMOND_BLASTX } from '../../modules/nf-core/diamond/blastx/main'
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include { MOTUS_PROFILE } from '../../modules/nf-core/motus/profile/main'
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include { KRAKENUNIQ_PRELOADEDKRAKENUNIQ } from '../../modules/nf-core/krakenuniq/preloadedkrakenuniq/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 { KRAKEN2_KRAKEN2 } from '../../modules/nf-core/kraken2/kraken2/main'
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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 { 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 { METAPHLAN3_METAPHLAN3 } from '../../modules/nf-core/metaphlan3/metaphlan3/main'
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include { KAIJU_KAIJU } from '../../modules/nf-core/kaiju/kaiju/main'
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include { KAIJU_KAIJU2TABLE as KAIJU_KAIJU2TABLE_SINGLE } from '../../modules/nf-core/kaiju/kaiju2table/main'
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include { DIAMOND_BLASTX } from '../../modules/nf-core/diamond/blastx/main'
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include { MOTUS_PROFILE } from '../../modules/nf-core/motus/profile/main'
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include { KRAKENUNIQ_PRELOADEDKRAKENUNIQ } from '../../modules/nf-core/krakenuniq/preloadedkrakenuniq/main'
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workflow PROFILING {
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take:
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@ -3,7 +3,7 @@
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//
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include { BRACKEN_COMBINEBRACKENOUTPUTS } from '../../modules/nf-core/bracken/combinebrackenoutputs/main'
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include { KAIJU_KAIJU2TABLE } from '../../modules/nf-core/kaiju/kaiju2table/main'
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include { KAIJU_KAIJU2TABLE as KAIJU_KAIJU2TABLE_COMBINED } from '../../modules/nf-core/kaiju/kaiju2table/main'
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include { KRAKENTOOLS_COMBINEKREPORTS as KRAKENTOOLS_COMBINEKREPORTS_KRAKEN } from '../../modules/nf-core/krakentools/combinekreports/main'
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include { KRAKENTOOLS_COMBINEKREPORTS as KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE } from '../../modules/nf-core/krakentools/combinekreports/main'
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include { METAPHLAN3_MERGEMETAPHLANTABLES } from '../../modules/nf-core/metaphlan3/mergemetaphlantables/main'
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@ -103,9 +103,9 @@ workflow STANDARDISATION_PROFILES {
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[[id:it[0]], it[1]]
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}
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KAIJU_KAIJU2TABLE ( ch_profiles_for_kaiju, ch_input_databases.kaiju.map{it[1]}, params.kaiju_taxon_rank)
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ch_multiqc_files = ch_multiqc_files.mix( KAIJU_KAIJU2TABLE.out.summary )
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ch_versions = ch_versions.mix( KAIJU_KAIJU2TABLE.out.versions )
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KAIJU_KAIJU2TABLE_COMBINED ( ch_profiles_for_kaiju, ch_input_databases.kaiju.map{it[1]}, params.kaiju_taxon_rank)
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ch_multiqc_files = ch_multiqc_files.mix( KAIJU_KAIJU2TABLE_COMBINED.out.summary )
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ch_versions = ch_versions.mix( KAIJU_KAIJU2TABLE_COMBINED.out.versions )
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// Kraken2
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@ -151,7 +151,7 @@ workflow STANDARDISATION_PROFILES {
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MOTUS_MERGE ( ch_profiles_for_motus, ch_input_databases.motus.map{it[1]}, motu_version )
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ch_versions = ch_versions.mix( MOTUS_MERGE.out.versions )
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emit:
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taxpasta = TAXPASTA_MERGE.out.merged_profiles
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versions = ch_versions
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