From 4165b91d847c1fdc461c2142e0f97b42b4aa849b Mon Sep 17 00:00:00 2001
From: MaxUlysse <max.u.garcia@gmail.com>
Date: Thu, 31 Jan 2019 10:08:06 +0100
Subject: [PATCH 1/2] remove old unused channels, and do the QC on the
 recalibrated bams

---
 main.nf | 15 ++++-----------
 1 file changed, 4 insertions(+), 11 deletions(-)

diff --git a/main.nf b/main.nf
index 866221bdfa..c96b4cf82e 100644
--- a/main.nf
+++ b/main.nf
@@ -379,15 +379,6 @@ if (params.verbose) recalibrationTable = recalibrationTable.view {
   Files : [${it[3].fileName}, ${it[4].fileName}, ${it[5].fileName}]"
 }
 
-(bamForBamQC, bamForSamToolsStats, recalTables, recalibrationTableForHC, recalibrationTable) = recalibrationTable.into(5)
-
-// Remove recalTable from Channels to match inputs for Process to avoid:
-// WARN: Input tuple does not match input set cardinality declared by process...
-bamForBamQC = bamForBamQC.map { it[0..4] }
-bamForSamToolsStats = bamForSamToolsStats.map{ it[0..4] }
-
-recalTables = recalTables.map { [it[0]] + it[2..-1] } // remove status
-
 process RecalibrateBam {
   tag {idPatient + "-" + idSample}
 
@@ -406,8 +397,6 @@ process RecalibrateBam {
     set idPatient, status, idSample, file("${idSample}.recal.bam"), file("${idSample}.recal.bai") into recalibratedBam, recalibratedBamForStats
     set idPatient, status, idSample, val("${idSample}.recal.bam"), val("${idSample}.recal.bai") into recalibratedBamTSV
 
-  // GATK4 HaplotypeCaller can not do BQSR on the fly, so we have to create a
-  // recalibrated BAM explicitly.
   when: !params.onlyQC
 
   script:
@@ -436,6 +425,10 @@ if (params.verbose) recalibratedBam = recalibratedBam.view {
   Files : [${it[3].fileName}, ${it[4].fileName}]"
 }
 
+// Remove recalTable from Channels to match inputs for Process to avoid:
+// WARN: Input tuple does not match input set cardinality declared by process...
+(bamForBamQC, bamForSamToolsStats) = recalibratedBamForStats.map{ it[0..4] }.into(2)
+
 process RunSamtoolsStats {
   tag {idPatient + "-" + idSample}
 

From 974c810361a7adacd1daf5ff4a6ed386dc7b5c6f Mon Sep 17 00:00:00 2001
From: MaxUlysse <max.u.garcia@gmail.com>
Date: Thu, 31 Jan 2019 10:14:19 +0100
Subject: [PATCH 2/2] update CHANGELOG

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

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 1d39de4fd2..ee38b4d9b7 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -16,6 +16,9 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 ### `Removed`
 -   [#715](https://github.com/SciLifeLab/Sarek/pull/715) - Remove `defReferencesFiles` function from `buildReferences.nf`
 
+### `Fixed`
+-   [#720](https://github.com/SciLifeLab/Sarek/pull/720) - bamQC is now run on the recalibrated bams, and not after MarkDuplicates
+
 ## [2.2.2] - 2018-12-19
 
 ### `Added`