Merge pull request #647 from genomic-medicine-sweden/add-fastp-to-mul…

…tiqc

add fastp and ngsbits to multiqc input

CHANGELOG.md

@@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - A new analysis option `mito` to call and annotate only mitochondrial variants [#608](https://github.com/nf-core/raredisease/pull/608)
 - An option to restrict analysis to specific contigs [#644](https://github.com/nf-core/raredisease/pull/644)
+- Fastp and ngsbits output files as input of MultiQC [#647](https://github.com/nf-core/raredisease/pull/647/).
 
 ### `Changed`
 

assets/multiqc_config.yml

@@ -22,6 +22,7 @@ run_modules:
   - qualimap
   - picard
   - mosdepth
+  - ngsbits
   - peddy
   - custom_content
 
@@ -38,6 +39,8 @@ module_order:
       name: "fastp"
   - mosdepth:
       name: "Mosdepth"
+  - ngsbits:
+      name: "ngsbits"
   - peddy:
       name: "Peddy"
 

workflows/raredisease.nf

@@ -902,6 +902,8 @@ workflow RAREDISEASE {
     )
 
     ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
+    ch_multiqc_files = ch_multiqc_files.mix(ALIGN.out.fastp_json.map{it[1]}.collect().ifEmpty([]))
+    ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.sex_check.map{it[1]}.collect().ifEmpty([]))
     ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.multiple_metrics.map{it[1]}.collect().ifEmpty([]))
     ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.hs_metrics.map{it[1]}.collect().ifEmpty([]))
     ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.qualimap_results.map{it[1]}.collect().ifEmpty([]))