Define separte krakena nd centrigfue modules

assets/multiqc_config.yml

@@ -28,20 +28,25 @@ run_modules:
 #    - '.se.settings'
 
 top_modules:
-  - 'fastqc':
-    name: "FastQC (pre-processing)"
-    path_filters:
-      - '*_raw.zip'
-  - 'fastp'
-  - 'fastqc':
-    name: "FastQC (post-processing)"
-    path_filters:
-      - '*_processed.zip'
-  - 'kraken':
-    name: "Kraken"
-    path_filters:
-      - '*kraken.report'
-  - 'kraken':
-    name: Centrifuge"
-    path_filters:
-      - '*centrifuge.kreport'
+    - 'fastqc':
+        name: 'FastQC (pre-Trimming)'
+        path_filters:
+            - '*raw_*fastqc.zip'
+    - 'fastp'
+    - 'adapterRemoval'
+    - 'fastqc':
+        name: 'FastQC (post-Trimming)'
+        path_filters:
+            - '*raw_*processed.zip'
+    - 'kraken':
+        name: 'Kraken'
+        path_filters:
+            - '*.kraken2.report.txt'
+    - 'kraken':
+        name: 'Centrifuge'
+        anchor: 'centrifuge'
+        target: 'Centrifuge'
+        doi: '10.1101/gr.210641.116'
+        info: "Centrifuge is a very rapid and memory-efficient system for the classification of DNA sequences from microbial samples. The system uses a novel indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index."
+        path_filters:
+            - '*.centrifuge.txt'

conf/modules.config

@@ -285,7 +285,7 @@ process {
 
     withName: KRAKEN2_KRAKEN2 {
         ext.args = { "${meta.db_params}" }
-        ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}.kraken" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}.kraken" }
+        ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
         publishDir = [
             path: { "${params.outdir}/kraken2/${meta.db_name}" },
             mode: params.publish_dir_mode,