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Add centrigue kreports

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This commit is contained in:
James Fellows Yates 2022-09-13 16:47:19 +02:00
parent c8dbf5be47
commit 05e9d92444
2 changed files with 35 additions and 5 deletions
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13
conf/modules.config
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@ -295,7 +295,7 @@ process {
} }
withName: KRAKENTOOLS_COMBINEKREPORTS { withName: KRAKENTOOLS_COMBINEKREPORTS {
ext.prefix = { "${meta.id}_combined_reports" } ext.prefix = { "kraken2_${meta.id}_combined_reports" }
publishDir = [ publishDir = [
path: { "${params.outdir}/kraken2/" }, path: { "${params.outdir}/kraken2/" },
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
@ -367,6 +367,15 @@ process {
] ]
} }
withName: KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE {
ext.prefix = { "centrifuge_${meta.id}_combined_reports" }
publishDir = [
path: { "${params.outdir}/centrifuge/" },
mode: params.publish_dir_mode,
pattern: '*.{txt}'
]
}
withName: KAIJU_KAIJU { withName: KAIJU_KAIJU {
ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" } ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
publishDir = [ publishDir = [
@ -378,7 +387,7 @@ process {
} }
withName: KAIJU_KAIJU2TABLE { withName: KAIJU_KAIJU2TABLE {
ext.prefix = { "${meta.id}_combined_reports" } ext.prefix = { "kaiju_${meta.id}_combined_reports" }
publishDir = [ publishDir = [
path: { "${params.outdir}/kaiju/" }, path: { "${params.outdir}/kaiju/" },
mode: params.publish_dir_mode, mode: params.publish_dir_mode,

27
subworkflows/local/standardisation_profiles.nf
View file

@ -2,9 +2,10 @@
// Standardise output files e.g. aggregation // Standardise output files e.g. aggregation
// //
include { KAIJU_KAIJU2TABLE } from '../../modules/nf-core/modules/kaiju/kaiju2table/main' include { KRAKENTOOLS_COMBINEKREPORTS as KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE } from '../../modules/nf-core/modules/krakentools/combinekreports/main'
include { KRAKENTOOLS_COMBINEKREPORTS } from '../../modules/nf-core/modules/krakentools/combinekreports/main' include { KAIJU_KAIJU2TABLE } from '../../modules/nf-core/modules/kaiju/kaiju2table/main'
include { MOTUS_MERGE } from '../../modules/nf-core/modules/motus/merge/main' include { KRAKENTOOLS_COMBINEKREPORTS } from '../../modules/nf-core/modules/krakentools/combinekreports/main'
include { MOTUS_MERGE } from '../../modules/nf-core/modules/motus/merge/main'
workflow STANDARDISATION_PROFILES { workflow STANDARDISATION_PROFILES {
take: take:
@ -25,6 +26,7 @@ workflow STANDARDISATION_PROFILES {
.branch { .branch {
motus: it[0]['tool'] == 'motus' motus: it[0]['tool'] == 'motus'
kraken2: it[0]['tool'] == 'kraken2' kraken2: it[0]['tool'] == 'kraken2'
centrifuge: it[0]['tool'] == 'centrifuge'
unknown: true unknown: true
} }
@ -45,6 +47,23 @@ workflow STANDARDISATION_PROFILES {
Standardise and aggregate Standardise and aggregate
*/ */
// CENTRIFUGE
// Collect and replace id for db_name for prefix
// Have to sort by size to ensure first file actually has hits otherwise
// the script fails
ch_profiles_for_centrifuge = ch_input_profiles.centrifuge
.map { [it[0]['db_name'], it[1]] }
.groupTuple(sort: {-it.size()} )
.map {
[[id:it[0]], it[1]]
}
KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE ( ch_profiles_for_centrifuge )
ch_standardised_tables = ch_standardised_tables.mix( KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE.out.txt )
ch_multiqc_files = ch_multiqc_files.mix( KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE.out.txt )
ch_versions = ch_versions.mix( KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE.out.versions )
// Kaiju // Kaiju
// Collect and replace id for db_name for prefix // Collect and replace id for db_name for prefix
@ -63,6 +82,8 @@ workflow STANDARDISATION_PROFILES {
// Kraken2 // Kraken2
// Collect and replace id for db_name for prefix // Collect and replace id for db_name for prefix
// Have to sort by size to ensure first file actually has hits otherwise
// the script fails
ch_profiles_for_kraken2 = ch_input_profiles.kraken2 ch_profiles_for_kraken2 = ch_input_profiles.kraken2
.map { [it[0]['db_name'], it[1]] } .map { [it[0]['db_name'], it[1]] }
.groupTuple(sort: {-it.size()} ) .groupTuple(sort: {-it.size()} )