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Fix ugly warn when KAIJU2TABLE not run

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This commit is contained in:
James Fellows Yates 2023-03-06 08:17:50 +01:00
parent f0f89eb082
commit a5138ed6e0
3 changed files with 20 additions and 20 deletions
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4
conf/modules.config
View file

@ -486,7 +486,7 @@ process {
ext.args = { "${meta.db_params}" } ext.args = { "${meta.db_params}" }
} }
withName: '.*PROFILING:KAIJU_KAIJU2TABLE' { withName: 'KAIJU_KAIJU2TABLE_SINGLE' {
ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.kaijutable" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.kaijutable" } ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.kaijutable" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.kaijutable" }
publishDir = [ publishDir = [
path: { "${params.outdir}/kaiju/${meta.db_name}/" }, path: { "${params.outdir}/kaiju/${meta.db_name}/" },
@ -495,7 +495,7 @@ process {
] ]
} }
withName: '.*STANDARDISATION_PROFILES:KAIJU_KAIJU2TABLE' { withName: 'KAIJU_KAIJU2TABLE_COMBINED' {
ext.prefix = { "kaiju_${meta.id}_combined_reports" } ext.prefix = { "kaiju_${meta.id}_combined_reports" }
publishDir = [ publishDir = [
path: { "${params.outdir}/kaiju/" }, path: { "${params.outdir}/kaiju/" },

26
subworkflows/local/profiling.nf
View file

@ -2,19 +2,19 @@
// Run profiling // Run profiling
// //
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 { KRAKEN2_STANDARD_REPORT } from '../../modules/local/kraken2_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'
include { METAPHLAN3_METAPHLAN3 } from '../../modules/nf-core/metaphlan3/metaphlan3/main' include { METAPHLAN3_METAPHLAN3 } from '../../modules/nf-core/metaphlan3/metaphlan3/main'
include { KAIJU_KAIJU } from '../../modules/nf-core/kaiju/kaiju/main' include { KAIJU_KAIJU } from '../../modules/nf-core/kaiju/kaiju/main'
include { KAIJU_KAIJU2TABLE } from '../../modules/nf-core/kaiju/kaiju2table/main' include { KAIJU_KAIJU2TABLE as KAIJU_KAIJU2TABLE_SINGLE } from '../../modules/nf-core/kaiju/kaiju2table/main'
include { DIAMOND_BLASTX } from '../../modules/nf-core/diamond/blastx/main' include { DIAMOND_BLASTX } from '../../modules/nf-core/diamond/blastx/main'
include { MOTUS_PROFILE } from '../../modules/nf-core/motus/profile/main' include { MOTUS_PROFILE } from '../../modules/nf-core/motus/profile/main'
include { KRAKENUNIQ_PRELOADEDKRAKENUNIQ } from '../../modules/nf-core/krakenuniq/preloadedkrakenuniq/main' include { KRAKENUNIQ_PRELOADEDKRAKENUNIQ } from '../../modules/nf-core/krakenuniq/preloadedkrakenuniq/main'
workflow PROFILING { workflow PROFILING {
take: take:

10
subworkflows/local/standardisation_profiles.nf
View file

@ -3,7 +3,7 @@
// //
include { BRACKEN_COMBINEBRACKENOUTPUTS } from '../../modules/nf-core/bracken/combinebrackenoutputs/main' include { BRACKEN_COMBINEBRACKENOUTPUTS } from '../../modules/nf-core/bracken/combinebrackenoutputs/main'
include { KAIJU_KAIJU2TABLE } from '../../modules/nf-core/kaiju/kaiju2table/main' include { KAIJU_KAIJU2TABLE as KAIJU_KAIJU2TABLE_COMBINED } from '../../modules/nf-core/kaiju/kaiju2table/main'
include { KRAKENTOOLS_COMBINEKREPORTS as KRAKENTOOLS_COMBINEKREPORTS_KRAKEN } from '../../modules/nf-core/krakentools/combinekreports/main' include { KRAKENTOOLS_COMBINEKREPORTS as KRAKENTOOLS_COMBINEKREPORTS_KRAKEN } from '../../modules/nf-core/krakentools/combinekreports/main'
include { KRAKENTOOLS_COMBINEKREPORTS as KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE } from '../../modules/nf-core/krakentools/combinekreports/main' include { KRAKENTOOLS_COMBINEKREPORTS as KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE } from '../../modules/nf-core/krakentools/combinekreports/main'
include { METAPHLAN3_MERGEMETAPHLANTABLES } from '../../modules/nf-core/metaphlan3/mergemetaphlantables/main' include { METAPHLAN3_MERGEMETAPHLANTABLES } from '../../modules/nf-core/metaphlan3/mergemetaphlantables/main'
@ -103,9 +103,9 @@ workflow STANDARDISATION_PROFILES {
[[id:it[0]], it[1]] [[id:it[0]], it[1]]
} }
KAIJU_KAIJU2TABLE ( ch_profiles_for_kaiju, ch_input_databases.kaiju.map{it[1]}, params.kaiju_taxon_rank) KAIJU_KAIJU2TABLE_COMBINED ( ch_profiles_for_kaiju, ch_input_databases.kaiju.map{it[1]}, params.kaiju_taxon_rank)
ch_multiqc_files = ch_multiqc_files.mix( KAIJU_KAIJU2TABLE.out.summary ) ch_multiqc_files = ch_multiqc_files.mix( KAIJU_KAIJU2TABLE_COMBINED.out.summary )
ch_versions = ch_versions.mix( KAIJU_KAIJU2TABLE.out.versions ) ch_versions = ch_versions.mix( KAIJU_KAIJU2TABLE_COMBINED.out.versions )
// Kraken2 // Kraken2
@ -151,7 +151,7 @@ workflow STANDARDISATION_PROFILES {
MOTUS_MERGE ( ch_profiles_for_motus, ch_input_databases.motus.map{it[1]}, motu_version ) MOTUS_MERGE ( ch_profiles_for_motus, ch_input_databases.motus.map{it[1]}, motu_version )
ch_versions = ch_versions.mix( MOTUS_MERGE.out.versions ) ch_versions = ch_versions.mix( MOTUS_MERGE.out.versions )
emit: emit:
taxpasta = TAXPASTA_MERGE.out.merged_profiles taxpasta = TAXPASTA_MERGE.out.merged_profiles
versions = ch_versions versions = ch_versions