Merge pull request #109 from nf-core/centrifuge_mqc

Trying to get Centrifuge output into MQC

assets/multiqc_config.yml

@@ -13,3 +13,41 @@ export_plots: true
 custom_logo: "nf-core-taxprofiler_logo_custom_light.png"
 custom_logo_url: https://nf-co.re/taxprofiler
 custom_logo_title: "nf-core/taxprofiler"
+
+run_modules:
+  - fastqc
+  - adapterRemoval
+  - fastp
+  - bowtie2
+  - kraken
+  - malt
+
+#extra_fn_clean_exts:
+#    - '_fastp'
+#    - '.pe.settings'
+#    - '.se.settings'
+
+top_modules:
+  - "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: "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. Note: Figure title"
+      extra: "Note: plot title will say Kraken2 due to Centrifuge producing the same output format as Kraken. If activated, see the actual Kraken2 results in the section above."
+      path_filters:
+        - "*.centrifuge.txt"

conf/modules.config

@@ -343,13 +343,13 @@ process {
             pattern: '*.{txt,sam,gz}'
         ]
         ext.args = { "${meta.db_params}" }
-        ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
+        ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}.centrifuge" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}.centrifuge" }
     }
 
     withName: CENTRIFUGE_KREPORT {
         errorStrategy = {task.exitStatus == 255 ? 'ignore' : 'retry'}
         ext.args = { "${meta.db_params}" }
-        ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
+        ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}.centrifuge" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}.centrifuge" }
         publishDir = [
             path: { "${params.outdir}/centrifuge/${meta.db_name}" },
             mode: params.publish_dir_mode,

subworkflows/local/profiling.nf

@@ -152,6 +152,7 @@ workflow PROFILING {
         ch_versions            = ch_versions.mix( CENTRIFUGE_CENTRIFUGE.out.versions.first() )
         ch_raw_classifications = ch_raw_classifications.mix( CENTRIFUGE_CENTRIFUGE.out.results )
         ch_raw_profiles        = ch_raw_profiles.mix( CENTRIFUGE_KREPORT.out.kreport )
+        ch_multiqc_files       = ch_multiqc_files.mix( CENTRIFUGE_KREPORT.out.kreport )
 
     }
 
@@ -185,7 +186,7 @@ workflow PROFILING {
 
         KAIJU_KAIJU ( ch_input_for_kaiju.reads, ch_input_for_kaiju.db)
         KAIJU_KAIJU2TABLE (KAIJU_KAIJU.out.results, ch_input_for_kaiju.db, params.kaiju_taxon_name)
-        ch_multiqc_files = ch_multiqc_files.mix( KAIJU_KAIJU2TABLE.out.summary  )
+        ch_multiqc_files = ch_multiqc_files.mix( KAIJU_KAIJU2TABLE.out.summary )
         ch_versions = ch_versions.mix( KAIJU_KAIJU.out.versions.first() )
         ch_raw_classifications = ch_raw_classifications.mix( KAIJU_KAIJU.out.results )
         ch_raw_profiles = ch_raw_profiles.mix( KAIJU_KAIJU2TABLE.out.summary )