From 5597c93254e371a46f665965ae95ed838c1b76df Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alex.peltzer@gmail.com>
Date: Thu, 25 Apr 2019 16:19:34 +0200
Subject: [PATCH 1/4] Use the BED file

---
 CHANGELOG.md | 1 +
 main.nf      | 3 +++
 2 files changed, 4 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index b054d81161..2739a2f75f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -37,6 +37,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 -   [#788](https://github.com/SciLifeLab/Sarek/pull/788) - Fix `genome_base` path in `munin.config`
 -   [#788](https://github.com/SciLifeLab/Sarek/pull/788) - Fix `markdup_java_options` definition
 -   [#788](https://github.com/SciLifeLab/Sarek/pull/788) - Include `conf/resources.config` in `btb` profile
+-   [#890](https://github.com/SciLifeLab/Sarek/pull/788) - Use BED file for [QualiMap coverage calculation](https://github.com/SciLifeLab/Sarek/issues/794) on Targeted Data
 
 ## [2.3.FIX1] - 2019-03-04
 
diff --git a/main.nf b/main.nf
index 23a515c70d..42d8c46c35 100644
--- a/main.nf
+++ b/main.nf
@@ -207,6 +207,7 @@ process RunBamQCmapped {
 
   input:
     set idPatient, status, idSample, idRun, file(bam) from mappedBamForQC
+    file(targetBED) from Channel.value(params.targetBED ? file(params.targetBED) : "null")
 
   output:
     file("${bam.baseName}") into bamQCmappedReport
@@ -214,12 +215,14 @@ process RunBamQCmapped {
   when: !params.noReports && !params.noBAMQC
 
   script:
+  use_bed = params.targetBED ?: "-gff ${targetBED}" : ''
   """
   qualimap --java-mem-size=${task.memory.toGiga()}G \
   bamqc \
   -bam ${bam} \
   --paint-chromosome-limits \
   --genome-gc-distr HUMAN \
+  $use_bed \
   -nt ${task.cpus} \
   -skip-duplicated \
   --skip-dup-mode 0 \

From d7e7b00098f134aac20624463992c84ba9e9148b Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alex.peltzer@gmail.com>
Date: Thu, 25 Apr 2019 16:21:38 +0200
Subject: [PATCH 2/4] Update Changelog [skip ci]

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 2739a2f75f..01423bc089 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -37,7 +37,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 -   [#788](https://github.com/SciLifeLab/Sarek/pull/788) - Fix `genome_base` path in `munin.config`
 -   [#788](https://github.com/SciLifeLab/Sarek/pull/788) - Fix `markdup_java_options` definition
 -   [#788](https://github.com/SciLifeLab/Sarek/pull/788) - Include `conf/resources.config` in `btb` profile
--   [#890](https://github.com/SciLifeLab/Sarek/pull/788) - Use BED file for [QualiMap coverage calculation](https://github.com/SciLifeLab/Sarek/issues/794) on Targeted Data
+-   [#795](https://github.com/SciLifeLab/Sarek/pull/795) - Use BED file for [QualiMap coverage calculation](https://github.com/SciLifeLab/Sarek/issues/794) on Targeted Data
 
 ## [2.3.FIX1] - 2019-03-04
 

From 1ad56426f9c360edf6d8524972681f398157ed0d Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alex.peltzer@gmail.com>
Date: Thu, 25 Apr 2019 16:24:33 +0200
Subject: [PATCH 3/4] Add targetBed to docs

---
 docs/USE_CASES.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/docs/USE_CASES.md b/docs/USE_CASES.md
index 259a2bfe4a..7389038e83 100644
--- a/docs/USE_CASES.md
+++ b/docs/USE_CASES.md
@@ -170,8 +170,8 @@ In this case, you need to start with `--step=recalibrate` (see previous section)
 
 ## Processing targeted (whole exome or panel) sequencing data
 
-The recommended flow for thrgeted sequencing data is to use the whole genome workflow as it is, but also provide a BED file containing targets for variant calling.
-The Strelka part of the workflow will pick up these intervals, and activate the `--exome` flag to process deeper coverage. It is adviced to pad the variant calling
+The recommended flow for targeted sequencing data is to use the whole genome workflow as it is, but also provide a BED file containing targets for all steps using the `--targetBED` option. 
+The workflow will pick up these intervals, and activate the `--exome` flag to process deeper coverage. It is adviced to pad the variant calling
 regions (exons or the target) to some extent before submitting to the workflow. To add the target BED file configure the flow like:
 
 ```bash

From 83c7553d150b4a3f9e22aae908052d4643555254 Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alex.peltzer@gmail.com>
Date: Thu, 25 Apr 2019 17:04:17 +0200
Subject: [PATCH 4/4] Try fixing operator

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

diff --git a/main.nf b/main.nf
index 42d8c46c35..ab6e3487b1 100644
--- a/main.nf
+++ b/main.nf
@@ -215,7 +215,7 @@ process RunBamQCmapped {
   when: !params.noReports && !params.noBAMQC
 
   script:
-  use_bed = params.targetBED ?: "-gff ${targetBED}" : ''
+  use_bed = params.targetBED ? "-gff ${targetBED}" : ''
   """
   qualimap --java-mem-size=${task.memory.toGiga()}G \
   bamqc \