Fix mqc section orders

CHANGELOG.md

@@ -4,11 +4,10 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 
-## [Unpublished]
+## [Unpublished / Dev Branch]
 
-### `Added`
-* [#80](https://github.com/nf-core/eager/pull/80) - BWA Index file handling 
-* [#77](https://github.com/nf-core/eager/pull/77) - Lots of documentation updates by [@jfy133](https://github.com/jfy133)
+### `Fixed`
+* [#110](https://github.com/nf-core/eager/pull/110) - Fix for [MultiQC Missing Second FastQC report](https://github.com/nf-core/eager/issues/107)
 
 ## [2.0.3] - 2018-12-09
 

conf/multiqc_config.yaml

@@ -5,15 +5,24 @@ report_comment: >
 report_section_order:
     nf-core/eager-software-versions:
         order: -1000
-top_modules:
-    - fastqc:
+    fastqc:
+        after: 'nf-core/eager-software-versions'
         name: 'FastQC (raw)'
         path_filters:
-            - '*_preAR_fastqc.zip'
-    - fastqc:
+            - '*_fastqc.zip'
+    fastqc:
         name: 'FastQC (trimmed)'
         info: 'This section of the report shows FastQC results after adapter trimming.'
         target: ''
         path_filters:
-            - '*_postAR_fastqc.zip'
-
+            - '*combined.prefixed_fastqc.zip'
+    adapterRemoval:
+        after: 'fastqc'
+    Samtools:
+        after: 'adapterRemoval'
+    dedup:
+        after: 'Samtools'
+    qualimap:
+        after: 'dedup'
+    preseq:
+        after: 'qualimap'

main.nf

@@ -1010,7 +1010,8 @@ process multiqc {
 
     input:
     file multiqc_config
-    file ('fastqc/*') from ch_fastqc_results.collect().ifEmpty([])
+    file ('fastqc_raw/*') from ch_fastqc_results.collect().ifEmpty([])
+    file('fastqc/*') from ch_fastqc_after_clipping.collect().ifEmpty([])
     file ('software_versions/*') from software_versions_yaml.collect().ifEmpty([])
     file ('adapter_removal/*') from ch_adapterremoval_logs.collect().ifEmpty([])
     file ('idxstats/*') from ch_idxstats_for_multiqc.collect().ifEmpty([])