Update MultiQC config

Oscarvelcam · May 29, 2020 · 894857b · 894857b
1 parent da3cb03
commit 894857b
Show file tree

Hide file tree

Showing 2 changed files with 27 additions and 18 deletions.
diff --git a/assets/multiqc_config.yaml b/assets/multiqc_config.yaml
@@ -3,19 +3,20 @@ report_comment: >
     analysis pipeline. For information about how to interpret these results, please see the
     <a href="https://github.com/nf-core/atacseq/blob/master/docs/output.md" target="_blank">documentation</a>.
 
-export_plots: true
+data_format: 'yaml'
 
-fn_clean_exts:
-    - 'fastq.gz'
-    - '_trimmed'
-    - '_val'
-    - 'sorted.bam'
-    - '.Lb'
-    - 'mkD'
-    - 'clN'
-    - 'mLb'
-    - 'mRp'
-    - '_peaks'
+run_modules:
+    - custom_content
+    - fastqc
+    - cutadapt
+    - samtools
+    - picard
+    - preseq
+    - featureCounts
+    - deeptools
+
+exclude_modules:
+    - 'general_stats'
 
 module_order:
     - fastqc:
@@ -115,12 +116,22 @@ report_section_order:
         order: -2100
 
 custom_plot_config:
-    picard-insertsize:
+    picard_insert_size:
         cpswitch_c_active: False
         smooth_points: 1000
-
     featurecounts:
         cpswitch_c_active: False
-
     featurecounts-1:
         cpswitch_c_active: False
+
+extra_fn_clean_exts:
+    - 'fastq.gz'
+    - '_trimmed'
+    - '_val'
+    - 'sorted.bam'
+    - '.Lb'
+    - 'mkD'
+    - 'clN'
+    - 'mLb'
+    - 'mRp'
+    - '_peaks'
diff --git a/main.nf b/main.nf
@@ -2016,15 +2016,13 @@ process MULTIQC {
     output:
     file "*multiqc_report.html" into ch_multiqc_report
     file "*_data"
-    file "multiqc_plots"
 
     script:
     rtitle = custom_runName ? "--title \"$custom_runName\"" : ''
     rfilename = custom_runName ? "--filename " + custom_runName.replaceAll('\\W','_').replaceAll('_+','_') + "_multiqc_report" : ''
     custom_config_file = params.multiqc_config ? "--config $mqc_custom_config" : ''
     """
-    multiqc . -f $rtitle $rfilename $custom_config_file \\
-        -m custom_content -m fastqc -m cutadapt -m samtools -m picard -m preseq -m featureCounts -m deeptools
+    multiqc . -f $rtitle $rfilename $custom_config_file
     """
 }