Bring back code removed by mistake

Author: JoseEspinosa

assets/multiqc_config.yml

@@ -3,6 +3,66 @@ report_comment: >
   analysis pipeline. For information about how to interpret these results, please see the
   <a href="https://nf-co.re/chipseq/dev/docs/output" target="_blank">documentation</a>.
 
+data_format: "yaml"
+
+export_plots: true
+
+exclude_modules:
+  - "general_stats"
+
+module_order:
+  - fastqc:
+      name: "LIB: FastQC (raw)"
+      info: "This section of the report shows FastQC results before adapter trimming for individual libraries."
+      path_filters:
+        - "./fastqc/*.zip"
+  - cutadapt:
+      name: "LIB: cutadapt (trimmed)"
+      info: "This section of the report shows the length of trimmed reads by cutadapt for individual libraries."
+  - fastqc:
+      name: "LIB: FastQC (trimmed)"
+      info: "This section of the report shows FastQC results after adapter trimming for individual libraries."
+      path_filters:
+        - "./trimgalore/fastqc/*.zip"
+  - samtools:
+      name: "LIB: SAMTools"
+      info: "This section of the report shows SAMTools results for individual libraries."
+      path_filters:
+        - "./alignment/library/*"
+  - samtools:
+      name: "MERGED LIB: SAMTools (unfiltered)"
+      info: "This section of the report shows SAMTools results after merging libraries and before filtering."
+      path_filters:
+        - "./alignment/merged_library/unfiltered/*.mLb.mkD.sorted.bam*"
+  - picard:
+      name: "MERGED LIB: Picard (unfiltered)"
+      info: "This section of the report shows picard results after merging libraries and before filtering."
+      path_filters:
+        - "./alignment/merged_library/unfiltered/picard_metrics/*"
+  - preseq:
+      name: "MERGED LIB: Preseq (unfiltered)"
+      info: "This section of the report shows Preseq results after merging libraries and before filtering."
+  - samtools:
+      name: "MERGED LIB: SAMTools (filtered)"
+      info: "This section of the report shows SAMTools results after merging libraries and after filtering."
+      path_filters:
+        - "./alignment/merged_library/filtered/*.mLb.clN.sorted.bam*"
+  - picard:
+      name: "MERGED LIB: Picard (filtered)"
+      info: "This section of the report shows picard results after merging libraries and after filtering."
+      path_filters:
+        - "./alignment/merged_library/filtered/picard_metrics/*"
+  - deeptools:
+      name: "MERGED LIB: deepTools"
+      anchor: "mlib_deeptools"
+      info: "This section of the report shows ChIP-seq QC plots generated by deepTools."
+  - featureCounts:
+      name: "MERGED LIB: featureCounts"
+      anchor: "mlib_featurecounts"
+      info: "This section of the report shows featureCounts results for the number of reads assigned to merged library consensus peaks."
+      path_filters:
+        - "./macs3/featurecounts/*.summary"
+
 report_section_order:
   peak_count:
     before: mlib_deeptools