From b94bd7866cc7668d6265ca89a492b04378650d0d Mon Sep 17 00:00:00 2001
From: Maxime Garcia <max.u.garcia@gmail.com>
Date: Mon, 15 Oct 2018 17:36:55 +0200
Subject: [PATCH 1/2] input bam file has always the same name

---
 main.nf | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/main.nf b/main.nf
index f130b42e9d..2ddad4e215 100644
--- a/main.nf
+++ b/main.nf
@@ -233,12 +233,12 @@ process MarkDuplicates {
     }
 
   input:
-    set idPatient, status, idSample, file(bam) from mergedBam
+    set idPatient, status, idSample, file("${idSample}.bam") from mergedBam
 
   output:
     set idPatient, file("${idSample}_${status}.md.bam"), file("${idSample}_${status}.md.bai") into duplicateMarkedBams
     set idPatient, status, idSample, val("${idSample}_${status}.md.bam"), val("${idSample}_${status}.md.bai") into markDuplicatesTSV
-    file ("${bam}.metrics") into markDuplicatesReport
+    file ("${idSample}.bam.metrics") into markDuplicatesReport
 
   when: step == 'mapping' && !params.onlyQC
 
@@ -247,8 +247,8 @@ process MarkDuplicates {
   gatk --java-options -Xmx${task.memory.toGiga()}g \
   MarkDuplicates \
   --MAX_RECORDS_IN_RAM 50000 \
-  --INPUT ${bam} \
-  --METRICS_FILE ${bam}.metrics \
+  --INPUT ${idSample}.bam \
+  --METRICS_FILE ${idSample}.bam.metrics \
   --TMP_DIR . \
   --ASSUME_SORT_ORDER coordinate \
   --CREATE_INDEX true \

From d3889c3e0ed2035385fc63e38e85614cd0909ecc Mon Sep 17 00:00:00 2001
From: Maxime Garcia <max.u.garcia@gmail.com>
Date: Tue, 16 Oct 2018 10:00:01 +0200
Subject: [PATCH 2/2] update CHANGELOG [skip ci]

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

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6259904237..51aa88fd9d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,6 +11,10 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 -   [#663](https://github.com/SciLifeLab/Sarek/pull/663) - Update `do_release.sh` script
 
+### `Fixed`
+
+-   [#665](https://github.com/SciLifeLab/Sarek/pull/665) - Input bam file now has always the same name (whether it is from a single fastq pair or multiple) in the MarkDuplicates process, so metrics too
+
 ## [2.2.1] - 2018-10-04
 
 ### `Changed`