From 05e9d92444d4689c172d2df3176bf180482fa5aa Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Tue, 13 Sep 2022 16:47:19 +0200
Subject: [PATCH] Add centrigue kreports

---
 conf/modules.config                           | 13 +++++++--
 .../local/standardisation_profiles.nf         | 27 ++++++++++++++++---
 2 files changed, 35 insertions(+), 5 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index f31eff5..2dd163f 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -295,7 +295,7 @@ process {
     }
 
     withName: KRAKENTOOLS_COMBINEKREPORTS {
-        ext.prefix = { "${meta.id}_combined_reports" }
+        ext.prefix = { "kraken2_${meta.id}_combined_reports" }
         publishDir = [
             path: { "${params.outdir}/kraken2/" },
             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 {
         ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
         publishDir = [
@@ -378,7 +387,7 @@ process {
     }
 
     withName: KAIJU_KAIJU2TABLE {
-        ext.prefix = { "${meta.id}_combined_reports" }
+        ext.prefix = { "kaiju_${meta.id}_combined_reports" }
         publishDir = [
             path: { "${params.outdir}/kaiju/" },
             mode: params.publish_dir_mode,
diff --git a/subworkflows/local/standardisation_profiles.nf b/subworkflows/local/standardisation_profiles.nf
index 14fb718..269a22c 100644
--- a/subworkflows/local/standardisation_profiles.nf
+++ b/subworkflows/local/standardisation_profiles.nf
@@ -2,9 +2,10 @@
 // Standardise output files e.g. aggregation
 //
 
-include { KAIJU_KAIJU2TABLE                     } from '../../modules/nf-core/modules/kaiju/kaiju2table/main'
-include { KRAKENTOOLS_COMBINEKREPORTS           } from '../../modules/nf-core/modules/krakentools/combinekreports/main'
-include { MOTUS_MERGE                           } from '../../modules/nf-core/modules/motus/merge/main'
+include { KRAKENTOOLS_COMBINEKREPORTS as KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE } from '../../modules/nf-core/modules/krakentools/combinekreports/main'
+include { KAIJU_KAIJU2TABLE                                                     } from '../../modules/nf-core/modules/kaiju/kaiju2table/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 {
     take:
@@ -25,6 +26,7 @@ workflow STANDARDISATION_PROFILES {
         .branch {
             motus: it[0]['tool'] == 'motus'
             kraken2: it[0]['tool'] == 'kraken2'
+            centrifuge: it[0]['tool'] == 'centrifuge'
             unknown: true
         }
 
@@ -45,6 +47,23 @@ workflow STANDARDISATION_PROFILES {
         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
 
     // Collect and replace id for db_name for prefix
@@ -63,6 +82,8 @@ workflow STANDARDISATION_PROFILES {
     // Kraken2
 
     // 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
                                 .map { [it[0]['db_name'], it[1]] }
                                 .groupTuple(sort: {-it.size()} )