From e1436a287f466e91a5b1d983ed00b58de27f0b30 Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alex.peltzer@gmail.com>
Date: Sat, 15 Dec 2018 18:15:00 +0100
Subject: [PATCH 1/5] Fix issues with MQC section order

---
 conf/multiqc_config.yaml | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/conf/multiqc_config.yaml b/conf/multiqc_config.yaml
index f420a53ad..e5f7907f1 100644
--- a/conf/multiqc_config.yaml
+++ b/conf/multiqc_config.yaml
@@ -7,6 +7,7 @@ report_section_order:
         order: -1000
 top_modules:
     - fastqc:
+        after: 'nf-core/eager-software-versions'
         name: 'FastQC (raw)'
         path_filters:
             - '*_preAR_fastqc.zip'
@@ -16,4 +17,15 @@ top_modules:
         target: ''
         path_filters:
             - '*_postAR_fastqc.zip'
+    - adapterRemoval:
+        after: 'fastqc'
+    - Samtools:
+        after: 'adapterRemoval'
+    - dedup:
+        after: 'Samtools'
+    - qualimap:
+        after: 'dedup'
+    - preseq:
+        after: 'qualimap'
+
 

From ff76ef11f6e950d15cb0ff41cd9e04b2c648994a Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alex.peltzer@gmail.com>
Date: Sat, 15 Dec 2018 21:25:18 +0100
Subject: [PATCH 2/5] Use FastQC reports after clipping

---
 main.nf | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/main.nf b/main.nf
index b16c9e347..8899fea60 100644
--- a/main.nf
+++ b/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([])

From ec0c3b058cc0982403ff2233e39313cf989db37f Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alex.peltzer@gmail.com>
Date: Sat, 15 Dec 2018 21:43:12 +0100
Subject: [PATCH 3/5] Adapt pattern for multiqc report

---
 conf/multiqc_config.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/conf/multiqc_config.yaml b/conf/multiqc_config.yaml
index e5f7907f1..bc0b29d53 100644
--- a/conf/multiqc_config.yaml
+++ b/conf/multiqc_config.yaml
@@ -10,13 +10,13 @@ top_modules:
         after: 'nf-core/eager-software-versions'
         name: 'FastQC (raw)'
         path_filters:
-            - '*_preAR_fastqc.zip'
+            - '*_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:

From ec602061e4ed0198641f3300471d259d10e5254e Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alex.peltzer@gmail.com>
Date: Sat, 15 Dec 2018 21:58:17 +0100
Subject: [PATCH 4/5] Fix YAML for sorting

---
 conf/multiqc_config.yaml | 19 ++++++++-----------
 1 file changed, 8 insertions(+), 11 deletions(-)

diff --git a/conf/multiqc_config.yaml b/conf/multiqc_config.yaml
index bc0b29d53..eead293f7 100644
--- a/conf/multiqc_config.yaml
+++ b/conf/multiqc_config.yaml
@@ -5,27 +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:
             - '*_fastqc.zip'
-    - fastqc:
+    fastqc:
         name: 'FastQC (trimmed)'
         info: 'This section of the report shows FastQC results after adapter trimming.'
         target: ''
         path_filters:
             - '*combined.prefixed_fastqc.zip'
-    - adapterRemoval:
+    adapterRemoval:
         after: 'fastqc'
-    - Samtools:
+    Samtools:
         after: 'adapterRemoval'
-    - dedup:
+    dedup:
         after: 'Samtools'
-    - qualimap:
+    qualimap:
         after: 'dedup'
-    - preseq:
-        after: 'qualimap'
-
-
+    preseq:
+        after: 'qualimap'
\ No newline at end of file

From e3e37db877375c50e03c7654b1d6cc639f4134f4 Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alex.peltzer@gmail.com>
Date: Sat, 15 Dec 2018 22:11:00 +0100
Subject: [PATCH 5/5] Add Changelog details

---
 CHANGELOG.md | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 399feedd1..cb016e5e7 100644
--- a/CHANGELOG.md
+++ b/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