diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index afa6f3e176d497f25988c4fc0be7f277da846103..79d53fbe10f7f3de2152a3e94802c5862dd3c271 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -2,7 +2,7 @@ image: snakemake/snakemake:v5.9.1
 
 before_script:
   - apt update
-  - apt install -y unzip
+  - apt install -y unzip bedtools
   - pip install -r scripts/requirements.txt
 
 test:
diff --git a/tests/test_integration_workflow/.java/fonts/1.8.0_111/fcinfo-1-shi03.cluster.bc2.ch-Linux-3.10.0-862.14.4.el7.x86_64-en.properties b/tests/test_integration_workflow/.java/fonts/1.8.0_111/fcinfo-1-shi03.cluster.bc2.ch-Linux-3.10.0-862.14.4.el7.x86_64-en.properties
deleted file mode 100644
index 270b359742115fa3a7f00c42493a5359aa9a4787..0000000000000000000000000000000000000000
--- a/tests/test_integration_workflow/.java/fonts/1.8.0_111/fcinfo-1-shi03.cluster.bc2.ch-Linux-3.10.0-862.14.4.el7.x86_64-en.properties
+++ /dev/null
@@ -1,245 +0,0 @@
-#JDK Font Configuration Generated File: *Do Not Edit*
-#Tue Feb 04 14:17:33 UTC 2020
-monospaced.3.5.family=DejaVu Serif
-sansserif.0.7.family=DejaVu Serif
-serif.2.8.family=DejaVu Sans Mono
-serif.3.0.file=/usr/share/fonts/truetype/dejavu/DejaVuSerif-BoldItalic.ttf
-monospaced.0.6.family=DejaVu Serif
-serif.3.1.family=DejaVu Serif
-sansserif.1.0.family=DejaVu Sans
-serif.2.5.file=/usr/share/fonts/truetype/dejavu/DejaVuSansMono-Oblique.ttf
-sansserif.0.length=9
-serif.0.2.family=DejaVu Serif
-serif.3.4.file=/usr/share/fonts/truetype/dejavu/DejaVuSans-BoldOblique.ttf
-sansserif.2.3.family=DejaVu Sans
-serif.2.9.file=/usr/share/fonts/truetype/dejavu/DejaVuSans-Bold.ttf
-monospaced.0.1.file=/usr/share/fonts/truetype/dejavu/DejaVuSans.ttf
-monospaced.2.2.family=DejaVu Serif
-serif.2.5.family=DejaVu Sans Mono
-sansserif.1.3.file=/usr/share/fonts/truetype/dejavu/DejaVuSans-Oblique.ttf
-serif.3.8.file=/usr/share/fonts/truetype/dejavu/DejaVuSans.ttf
-monospaced.1.0.file=/usr/share/fonts/truetype/dejavu/DejaVuSansMono-Bold.ttf
-monospaced.0.5.file=/usr/share/fonts/truetype/dejavu/DejaVuSerif-Italic.ttf
-monospaced.1.length=9
-serif.3.8.family=DejaVu Sans
-sansserif.1.7.family=DejaVu Serif
-sansserif.2.2.file=/usr/share/fonts/truetype/dejavu/DejaVuSans.ttf
-monospaced.1.6.family=DejaVu Serif
-sansserif.1.7.file=/usr/share/fonts/truetype/dejavu/DejaVuSerif-BoldItalic.ttf
-serif.3.length=10
-sansserif.2.0.family=DejaVu Sans
-monospaced.1.4.file=/usr/share/fonts/truetype/dejavu/DejaVuSans.ttf
-serif.1.2.family=DejaVu Serif
-sansserif.3.1.file=/usr/share/fonts/truetype/dejavu/DejaVuSans-Oblique.ttf
-sansserif.2.6.file=/usr/share/fonts/truetype/dejavu/DejaVuSansMono-Oblique.ttf
-sansserif.3.3.family=DejaVu Sans
-monospaced.2.3.file=/usr/share/fonts/truetype/dejavu/DejaVuSerif-BoldItalic.ttf
-monospaced.3.2.family=DejaVu Sans Mono
-monospaced.1.8.file=/usr/share/fonts/truetype/dejavu/DejaVuSans-Oblique.ttf
-sansserif.0.4.family=DejaVu Sans Mono
-serif.3.5.family=DejaVu Sans Mono
-sansserif.3.5.file=/usr/share/fonts/truetype/dejavu/DejaVuSerif-Italic.ttf
-serif.0.0.file=/usr/share/fonts/truetype/dejavu/DejaVuSerif.ttf
-monospaced.0.3.family=DejaVu Sans
-serif.0.6.family=DejaVu Sans
-monospaced.3.2.file=/usr/share/fonts/truetype/dejavu/DejaVuSansMono-Bold.ttf
-serif.0.length=9
-monospaced.2.7.file=/usr/share/fonts/truetype/dejavu/DejaVuSans-Bold.ttf
-sansserif.0.1.file=/usr/share/fonts/truetype/dejavu/DejaVuSans-Bold.ttf
-sansserif.2.7.family=DejaVu Sans Mono
-serif.0.4.file=/usr/share/fonts/truetype/dejavu/DejaVuSans.ttf
-monospaced.2.6.family=DejaVu Sans
-serif.1.9.family=DejaVu Sans
-sansserif.3.0.family=DejaVu Sans
-monospaced.3.6.file=/usr/share/fonts/truetype/dejavu/DejaVuSans-BoldOblique.ttf
-sansserif.0.1.family=DejaVu Sans
-serif.2.2.family=DejaVu Serif
-serif.1.3.file=/usr/share/fonts/truetype/dejavu/DejaVuSerif-Italic.ttf
-sansserif.0.5.file=/usr/share/fonts/truetype/dejavu/DejaVuSerif.ttf
-monospaced.0.0.family=DejaVu Sans Mono
-serif.0.8.file=/usr/share/fonts/truetype/dejavu/DejaVuSans-BoldOblique.ttf
-monospaced.3.9.family=DejaVu Serif
-sansserif.1.4.family=DejaVu Sans Mono
-serif.2.2.file=/usr/share/fonts/truetype/dejavu/DejaVuSerif.ttf
-monospaced.1.3.family=DejaVu Serif
-serif.1.7.file=/usr/share/fonts/truetype/dejavu/DejaVuSansMono.ttf
-serif.1.6.family=DejaVu Sans
-serif.3.1.file=/usr/share/fonts/truetype/dejavu/DejaVuSerif-Italic.ttf
-sansserif.3.7.family=DejaVu Serif
-serif.2.6.file=/usr/share/fonts/truetype/dejavu/DejaVuSans-BoldOblique.ttf
-monospaced.3.6.family=DejaVu Sans
-sansserif.0.8.family=DejaVu Serif
-serif.2.9.family=DejaVu Sans
-sansserif.1.0.file=/usr/share/fonts/truetype/dejavu/DejaVuSans-Bold.ttf
-monospaced.0.7.family=DejaVu Sans
-serif.3.2.family=DejaVu Serif
-sansserif.1.1.family=DejaVu Sans
-serif.3.5.file=/usr/share/fonts/truetype/dejavu/DejaVuSansMono-BoldOblique.ttf
-sansserif.1.length=9
-monospaced.1.0.family=DejaVu Sans Mono
-serif.0.3.family=DejaVu Serif
-monospaced.0.2.file=/usr/share/fonts/truetype/dejavu/DejaVuSerif.ttf
-sansserif.1.4.file=/usr/share/fonts/truetype/dejavu/DejaVuSansMono-Bold.ttf
-sansserif.2.4.family=DejaVu Serif
-serif.3.9.file=/usr/share/fonts/truetype/dejavu/DejaVuSansMono.ttf
-monospaced.1.1.file=/usr/share/fonts/truetype/dejavu/DejaVuSansMono.ttf
-monospaced.2.3.family=DejaVu Serif
-monospaced.0.6.file=/usr/share/fonts/truetype/dejavu/DejaVuSerif-BoldItalic.ttf
-sansserif.2.3.file=/usr/share/fonts/truetype/dejavu/DejaVuSans-Bold.ttf
-sansserif.1.8.file=/usr/share/fonts/truetype/dejavu/DejaVuSerif-Italic.ttf
-monospaced.2.0.file=/usr/share/fonts/truetype/dejavu/DejaVuSansMono-Oblique.ttf
-serif.0.0.family=DejaVu Serif
-monospaced.1.5.file=/usr/share/fonts/truetype/dejavu/DejaVuSerif-BoldItalic.ttf
-monospaced.2.length=9
-serif.3.9.family=DejaVu Sans Mono
-sansserif.1.8.family=DejaVu Serif
-sansserif.3.2.file=/usr/share/fonts/truetype/dejavu/DejaVuSans-Bold.ttf
-version=1
-monospaced.1.7.family=DejaVu Sans
-sansserif.2.7.file=/usr/share/fonts/truetype/dejavu/DejaVuSansMono.ttf
-sansserif.2.1.family=DejaVu Sans
-monospaced.2.4.file=/usr/share/fonts/truetype/dejavu/DejaVuSans-Oblique.ttf
-monospaced.2.0.family=DejaVu Sans Mono
-serif.1.3.family=DejaVu Serif
-sansserif.3.6.file=/usr/share/fonts/truetype/dejavu/DejaVuSansMono-BoldOblique.ttf
-serif.0.1.file=/usr/share/fonts/truetype/dejavu/DejaVuSerif-Bold.ttf
-sansserif.3.4.family=DejaVu Serif
-monospaced.3.3.file=/usr/share/fonts/truetype/dejavu/DejaVuSansMono.ttf
-monospaced.3.3.family=DejaVu Sans Mono
-monospaced.2.8.file=/usr/share/fonts/truetype/dejavu/DejaVuSerif-Bold.ttf
-sansserif.0.5.family=DejaVu Serif
-serif.2.6.family=DejaVu Sans
-fcversion=21100
-serif.1.0.file=/usr/share/fonts/truetype/dejavu/DejaVuSerif-Bold.ttf
-sansserif.0.2.file=/usr/share/fonts/truetype/dejavu/DejaVuSans-Oblique.ttf
-monospaced.0.4.family=DejaVu Serif
-serif.0.5.file=/usr/share/fonts/truetype/dejavu/DejaVuSansMono.ttf
-serif.1.length=10
-monospaced.3.7.file=/usr/share/fonts/truetype/dejavu/DejaVuSans-Oblique.ttf
-serif.1.0.family=DejaVu Serif
-sansserif.0.6.file=/usr/share/fonts/truetype/dejavu/DejaVuSerif-Bold.ttf
-serif.1.4.file=/usr/share/fonts/truetype/dejavu/DejaVuSans-Bold.ttf
-sansserif.3.1.family=DejaVu Sans
-monospaced.3.0.family=DejaVu Sans Mono
-serif.2.3.family=DejaVu Serif
-sansserif.0.2.family=DejaVu Sans
-serif.2.3.file=/usr/share/fonts/truetype/dejavu/DejaVuSerif-Bold.ttf
-monospaced.0.1.family=DejaVu Sans
-serif.1.8.file=/usr/share/fonts/truetype/dejavu/DejaVuSans-BoldOblique.ttf
-cachedir.2=/scicore/home/zavolan/kanitz/SANDBOX/rnaseqpipeline/tests/test_integration_workflow/.fontconfig
-cachedir.1=/scicore/home/zavolan/kanitz/SANDBOX/rnaseqpipeline/tests/test_integration_workflow/.cache/fontconfig
-cachedir.0=/var/cache/fontconfig
-serif.3.6.family=DejaVu Sans
-sansserif.1.5.family=DejaVu Serif
-serif.3.2.file=/usr/share/fonts/truetype/dejavu/DejaVuSerif-Bold.ttf
-monospaced.1.4.family=DejaVu Sans
-serif.0.7.family=DejaVu Sans
-serif.2.7.file=/usr/share/fonts/truetype/dejavu/DejaVuSans.ttf
-sansserif.1.1.file=/usr/share/fonts/truetype/dejavu/DejaVuSans.ttf
-serif.2.0.family=DejaVu Serif
-sansserif.2.8.family=DejaVu Serif
-serif.3.6.file=/usr/share/fonts/truetype/dejavu/DejaVuSans-Oblique.ttf
-monospaced.2.7.family=DejaVu Sans
-monospaced.0.3.file=/usr/share/fonts/truetype/dejavu/DejaVuSans-Bold.ttf
-sansserif.2.0.file=/usr/share/fonts/truetype/dejavu/DejaVuSans-Oblique.ttf
-serif.3.3.family=DejaVu Serif
-sansserif.1.2.family=DejaVu Sans
-sansserif.1.5.file=/usr/share/fonts/truetype/dejavu/DejaVuSerif-Bold.ttf
-sansserif.2.length=9
-monospaced.1.1.family=DejaVu Sans Mono
-serif.0.4.family=DejaVu Sans
-monospaced.1.2.file=/usr/share/fonts/truetype/dejavu/DejaVuSans-Bold.ttf
-monospaced.0.7.file=/usr/share/fonts/truetype/dejavu/DejaVuSans-Oblique.ttf
-sansserif.2.4.file=/usr/share/fonts/truetype/dejavu/DejaVuSerif-Italic.ttf
-sansserif.2.5.family=DejaVu Serif
-monospaced.2.1.file=/usr/share/fonts/truetype/dejavu/DejaVuSansMono.ttf
-monospaced.2.4.family=DejaVu Sans
-serif.1.7.family=DejaVu Sans Mono
-monospaced.1.6.file=/usr/share/fonts/truetype/dejavu/DejaVuSerif-Italic.ttf
-sansserif.3.3.file=/usr/share/fonts/truetype/dejavu/DejaVuSans.ttf
-serif.3.0.family=DejaVu Serif
-sansserif.3.8.family=DejaVu Sans Mono
-sansserif.2.8.file=/usr/share/fonts/truetype/dejavu/DejaVuSerif-Bold.ttf
-monospaced.3.0.file=/usr/share/fonts/truetype/dejavu/DejaVuSansMono-BoldOblique.ttf
-serif.0.1.family=DejaVu Serif
-monospaced.3.7.family=DejaVu Sans
-monospaced.2.5.file=/usr/share/fonts/truetype/dejavu/DejaVuSans-BoldOblique.ttf
-monospaced.3.length=11
-monospaced.0.8.family=DejaVu Sans
-sansserif.3.7.file=/usr/share/fonts/truetype/dejavu/DejaVuSerif-Bold.ttf
-serif.0.2.file=/usr/share/fonts/truetype/dejavu/DejaVuSerif-Italic.ttf
-sansserif.2.2.family=DejaVu Sans
-monospaced.3.4.file=/usr/share/fonts/truetype/dejavu/DejaVuSerif-BoldItalic.ttf
-monospaced.2.1.family=DejaVu Sans Mono
-serif.1.4.family=DejaVu Sans
-serif.1.1.file=/usr/share/fonts/truetype/dejavu/DejaVuSerif.ttf
-sansserif.0.3.file=/usr/share/fonts/truetype/dejavu/DejaVuSans-BoldOblique.ttf
-serif.0.6.file=/usr/share/fonts/truetype/dejavu/DejaVuSans-Bold.ttf
-sansserif.3.5.family=DejaVu Serif
-monospaced.3.8.file=/usr/share/fonts/truetype/dejavu/DejaVuSans-Bold.ttf
-monospaced.3.4.family=DejaVu Serif
-sansserif.0.6.family=DejaVu Serif
-serif.2.7.family=DejaVu Sans
-serif.2.0.file=/usr/share/fonts/truetype/dejavu/DejaVuSerif-Italic.ttf
-monospaced.0.5.family=DejaVu Serif
-sansserif.0.7.file=/usr/share/fonts/truetype/dejavu/DejaVuSerif-Italic.ttf
-serif.1.5.file=/usr/share/fonts/truetype/dejavu/DejaVuSansMono-Bold.ttf
-serif.2.length=10
-monospaced.1.8.family=DejaVu Sans
-serif.2.4.file=/usr/share/fonts/truetype/dejavu/DejaVuSans-Oblique.ttf
-serif.1.9.file=/usr/share/fonts/truetype/dejavu/DejaVuSans-Oblique.ttf
-sansserif.0.3.family=DejaVu Sans
-serif.2.4.family=DejaVu Sans
-serif.3.3.file=/usr/share/fonts/truetype/dejavu/DejaVuSerif.ttf
-monospaced.0.2.family=DejaVu Serif
-serif.2.8.file=/usr/share/fonts/truetype/dejavu/DejaVuSansMono.ttf
-monospaced.0.0.file=/usr/share/fonts/truetype/dejavu/DejaVuSansMono.ttf
-monospaced.0.length=9
-serif.3.7.family=DejaVu Sans
-sansserif.1.6.family=DejaVu Sans Mono
-sansserif.1.2.file=/usr/share/fonts/truetype/dejavu/DejaVuSans-BoldOblique.ttf
-monospaced.1.5.family=DejaVu Serif
-serif.3.7.file=/usr/share/fonts/truetype/dejavu/DejaVuSans-Bold.ttf
-serif.0.8.family=DejaVu Sans
-monospaced.0.4.file=/usr/share/fonts/truetype/dejavu/DejaVuSerif-Bold.ttf
-monospaced.3.10.file=/usr/share/fonts/truetype/dejavu/DejaVuSans.ttf
-serif.1.1.family=DejaVu Serif
-sansserif.2.1.file=/usr/share/fonts/truetype/dejavu/DejaVuSans-BoldOblique.ttf
-sansserif.1.6.file=/usr/share/fonts/truetype/dejavu/DejaVuSansMono.ttf
-monospaced.2.8.family=DejaVu Serif
-sansserif.3.2.family=DejaVu Sans
-monospaced.1.3.file=/usr/share/fonts/truetype/dejavu/DejaVuSerif-Bold.ttf
-monospaced.3.1.family=DejaVu Sans Mono
-monospaced.0.8.file=/usr/share/fonts/truetype/dejavu/DejaVuSans-BoldOblique.ttf
-sansserif.3.0.file=/usr/share/fonts/truetype/dejavu/DejaVuSans-BoldOblique.ttf
-serif.3.4.family=DejaVu Sans
-sansserif.2.5.file=/usr/share/fonts/truetype/dejavu/DejaVuSerif-BoldItalic.ttf
-sansserif.3.length=9
-serif.0.5.family=DejaVu Sans Mono
-monospaced.2.2.file=/usr/share/fonts/truetype/dejavu/DejaVuSerif-Italic.ttf
-monospaced.1.7.file=/usr/share/fonts/truetype/dejavu/DejaVuSans-BoldOblique.ttf
-sansserif.3.4.file=/usr/share/fonts/truetype/dejavu/DejaVuSerif-BoldItalic.ttf
-sansserif.2.6.family=DejaVu Sans Mono
-monospaced.3.1.file=/usr/share/fonts/truetype/dejavu/DejaVuSansMono-Oblique.ttf
-monospaced.2.5.family=DejaVu Sans
-serif.1.8.family=DejaVu Sans
-monospaced.2.6.file=/usr/share/fonts/truetype/dejavu/DejaVuSans.ttf
-monospaced.3.10.family=DejaVu Sans
-serif.2.1.family=DejaVu Serif
-sansserif.0.0.file=/usr/share/fonts/truetype/dejavu/DejaVuSans.ttf
-sansserif.0.0.family=DejaVu Sans
-sansserif.3.8.file=/usr/share/fonts/truetype/dejavu/DejaVuSansMono.ttf
-serif.0.3.file=/usr/share/fonts/truetype/dejavu/DejaVuSerif-BoldItalic.ttf
-monospaced.3.8.family=DejaVu Sans
-monospaced.3.5.file=/usr/share/fonts/truetype/dejavu/DejaVuSerif-Italic.ttf
-sansserif.1.3.family=DejaVu Sans
-serif.1.2.file=/usr/share/fonts/truetype/dejavu/DejaVuSerif-BoldItalic.ttf
-sansserif.0.4.file=/usr/share/fonts/truetype/dejavu/DejaVuSansMono.ttf
-monospaced.1.2.family=DejaVu Sans
-serif.0.7.file=/usr/share/fonts/truetype/dejavu/DejaVuSans-Oblique.ttf
-serif.1.5.family=DejaVu Sans Mono
-monospaced.3.9.file=/usr/share/fonts/truetype/dejavu/DejaVuSerif-Bold.ttf
-serif.2.1.file=/usr/share/fonts/truetype/dejavu/DejaVuSerif-BoldItalic.ttf
-sansserif.3.6.family=DejaVu Sans Mono
-serif.1.6.file=/usr/share/fonts/truetype/dejavu/DejaVuSans.ttf
-sansserif.0.8.file=/usr/share/fonts/truetype/dejavu/DejaVuSerif-BoldItalic.ttf
diff --git a/tests/test_integration_workflow/.java/fonts/1.8.0_111/fcinfo-1-shi20.cluster.bc2.ch-Linux-3.10.0-862.14.4.el7.x86_64-en.properties b/tests/test_integration_workflow/.java/fonts/1.8.0_111/fcinfo-1-shi20.cluster.bc2.ch-Linux-3.10.0-862.14.4.el7.x86_64-en.properties
deleted file mode 100644
index dd359b621e3e83ecf601dd2891099e85cb555ce8..0000000000000000000000000000000000000000
--- a/tests/test_integration_workflow/.java/fonts/1.8.0_111/fcinfo-1-shi20.cluster.bc2.ch-Linux-3.10.0-862.14.4.el7.x86_64-en.properties
+++ /dev/null
@@ -1,245 +0,0 @@
-#JDK Font Configuration Generated File: *Do Not Edit*
-#Tue Feb 04 14:15:22 UTC 2020
-monospaced.3.5.family=DejaVu Serif
-sansserif.0.7.family=DejaVu Serif
-serif.2.8.family=DejaVu Sans Mono
-serif.3.0.file=/usr/share/fonts/truetype/dejavu/DejaVuSerif-BoldItalic.ttf
-monospaced.0.6.family=DejaVu Serif
-serif.3.1.family=DejaVu Serif
-sansserif.1.0.family=DejaVu Sans
-serif.2.5.file=/usr/share/fonts/truetype/dejavu/DejaVuSansMono-Oblique.ttf
-sansserif.0.length=9
-serif.0.2.family=DejaVu Serif
-serif.3.4.file=/usr/share/fonts/truetype/dejavu/DejaVuSans-BoldOblique.ttf
-sansserif.2.3.family=DejaVu Sans
-serif.2.9.file=/usr/share/fonts/truetype/dejavu/DejaVuSans-Bold.ttf
-monospaced.0.1.file=/usr/share/fonts/truetype/dejavu/DejaVuSans.ttf
-monospaced.2.2.family=DejaVu Serif
-serif.2.5.family=DejaVu Sans Mono
-sansserif.1.3.file=/usr/share/fonts/truetype/dejavu/DejaVuSans-Oblique.ttf
-serif.3.8.file=/usr/share/fonts/truetype/dejavu/DejaVuSans.ttf
-monospaced.1.0.file=/usr/share/fonts/truetype/dejavu/DejaVuSansMono-Bold.ttf
-monospaced.0.5.file=/usr/share/fonts/truetype/dejavu/DejaVuSerif-Italic.ttf
-monospaced.1.length=9
-serif.3.8.family=DejaVu Sans
-sansserif.1.7.family=DejaVu Serif
-sansserif.2.2.file=/usr/share/fonts/truetype/dejavu/DejaVuSans.ttf
-monospaced.1.6.family=DejaVu Serif
-sansserif.1.7.file=/usr/share/fonts/truetype/dejavu/DejaVuSerif-BoldItalic.ttf
-serif.3.length=10
-sansserif.2.0.family=DejaVu Sans
-monospaced.1.4.file=/usr/share/fonts/truetype/dejavu/DejaVuSans.ttf
-serif.1.2.family=DejaVu Serif
-sansserif.3.1.file=/usr/share/fonts/truetype/dejavu/DejaVuSans-Oblique.ttf
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-serif.2.1.file=/usr/share/fonts/truetype/dejavu/DejaVuSerif-BoldItalic.ttf
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-serif.1.6.file=/usr/share/fonts/truetype/dejavu/DejaVuSans.ttf
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diff --git a/tests/test_integration_workflow/.java/fonts/1.8.0_111/fcinfo-1-shi33.cluster.bc2.ch-Linux-3.10.0-862.14.4.el7.x86_64-en.properties b/tests/test_integration_workflow/.java/fonts/1.8.0_111/fcinfo-1-shi33.cluster.bc2.ch-Linux-3.10.0-862.14.4.el7.x86_64-en.properties
deleted file mode 100644
index 20526159a6869e870fdc7fd1ce299f942b776c4f..0000000000000000000000000000000000000000
--- a/tests/test_integration_workflow/.java/fonts/1.8.0_111/fcinfo-1-shi33.cluster.bc2.ch-Linux-3.10.0-862.14.4.el7.x86_64-en.properties
+++ /dev/null
@@ -1,245 +0,0 @@
-#JDK Font Configuration Generated File: *Do Not Edit*
-#Tue Feb 04 12:10:34 UTC 2020
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-serif.2.9.file=/usr/share/fonts/truetype/dejavu/DejaVuSans-Bold.ttf
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-serif.0.7.file=/usr/share/fonts/truetype/dejavu/DejaVuSans-Oblique.ttf
-serif.1.5.family=DejaVu Sans Mono
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-serif.1.6.file=/usr/share/fonts/truetype/dejavu/DejaVuSans.ttf
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diff --git a/tests/test_integration_workflow/.java/fonts/1.8.0_111/fcinfo-1-usi105.cluster.bc2.ch-Linux-3.10.0-862.14.4.el7.x86_64-en.properties b/tests/test_integration_workflow/.java/fonts/1.8.0_111/fcinfo-1-usi105.cluster.bc2.ch-Linux-3.10.0-862.14.4.el7.x86_64-en.properties
deleted file mode 100644
index 7605aed3c618c5309bd1877221a773ff7938770c..0000000000000000000000000000000000000000
--- a/tests/test_integration_workflow/.java/fonts/1.8.0_111/fcinfo-1-usi105.cluster.bc2.ch-Linux-3.10.0-862.14.4.el7.x86_64-en.properties
+++ /dev/null
@@ -1,245 +0,0 @@
-#JDK Font Configuration Generated File: *Do Not Edit*
-#Tue Feb 04 12:10:35 UTC 2020
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-serif.2.5.file=/usr/share/fonts/truetype/dejavu/DejaVuSansMono-Oblique.ttf
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-serif.3.4.file=/usr/share/fonts/truetype/dejavu/DejaVuSans-BoldOblique.ttf
-sansserif.2.3.family=DejaVu Sans
-serif.2.9.file=/usr/share/fonts/truetype/dejavu/DejaVuSans-Bold.ttf
-monospaced.0.1.file=/usr/share/fonts/truetype/dejavu/DejaVuSans.ttf
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diff --git a/tests/test_integration_workflow/.java/fonts/1.8.0_111/fcinfo-1-worker03.cluster.bc2.ch-Linux-3.10.0-862.14.4.el7.x86_64-en.properties b/tests/test_integration_workflow/.java/fonts/1.8.0_111/fcinfo-1-worker03.cluster.bc2.ch-Linux-3.10.0-862.14.4.el7.x86_64-en.properties
deleted file mode 100644
index 207503ef9ae7a90077a9d6b18352b4889edecb22..0000000000000000000000000000000000000000
--- a/tests/test_integration_workflow/.java/fonts/1.8.0_111/fcinfo-1-worker03.cluster.bc2.ch-Linux-3.10.0-862.14.4.el7.x86_64-en.properties
+++ /dev/null
@@ -1,245 +0,0 @@
-#JDK Font Configuration Generated File: *Do Not Edit*
-#Tue Feb 04 12:05:16 UTC 2020
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-monospaced.0.8.family=DejaVu Sans
-sansserif.3.7.file=/usr/share/fonts/truetype/dejavu/DejaVuSerif-Bold.ttf
-serif.0.2.file=/usr/share/fonts/truetype/dejavu/DejaVuSerif-Italic.ttf
-sansserif.2.2.family=DejaVu Sans
-monospaced.3.4.file=/usr/share/fonts/truetype/dejavu/DejaVuSerif-BoldItalic.ttf
-monospaced.2.1.family=DejaVu Sans Mono
-serif.1.4.family=DejaVu Sans
-serif.1.1.file=/usr/share/fonts/truetype/dejavu/DejaVuSerif.ttf
-sansserif.0.3.file=/usr/share/fonts/truetype/dejavu/DejaVuSans-BoldOblique.ttf
-serif.0.6.file=/usr/share/fonts/truetype/dejavu/DejaVuSans-Bold.ttf
-sansserif.3.5.family=DejaVu Serif
-monospaced.3.8.file=/usr/share/fonts/truetype/dejavu/DejaVuSans-Bold.ttf
-monospaced.3.4.family=DejaVu Serif
-sansserif.0.6.family=DejaVu Serif
-serif.2.7.family=DejaVu Sans
-serif.2.0.file=/usr/share/fonts/truetype/dejavu/DejaVuSerif-Italic.ttf
-monospaced.0.5.family=DejaVu Serif
-sansserif.0.7.file=/usr/share/fonts/truetype/dejavu/DejaVuSerif-Italic.ttf
-serif.1.5.file=/usr/share/fonts/truetype/dejavu/DejaVuSansMono-Bold.ttf
-serif.2.length=10
-monospaced.1.8.family=DejaVu Sans
-serif.2.4.file=/usr/share/fonts/truetype/dejavu/DejaVuSans-Oblique.ttf
-serif.1.9.file=/usr/share/fonts/truetype/dejavu/DejaVuSans-Oblique.ttf
-sansserif.0.3.family=DejaVu Sans
-serif.2.4.family=DejaVu Sans
-serif.3.3.file=/usr/share/fonts/truetype/dejavu/DejaVuSerif.ttf
-monospaced.0.2.family=DejaVu Serif
-serif.2.8.file=/usr/share/fonts/truetype/dejavu/DejaVuSansMono.ttf
-monospaced.0.0.file=/usr/share/fonts/truetype/dejavu/DejaVuSansMono.ttf
-monospaced.0.length=9
-serif.3.7.family=DejaVu Sans
-sansserif.1.6.family=DejaVu Sans Mono
-sansserif.1.2.file=/usr/share/fonts/truetype/dejavu/DejaVuSans-BoldOblique.ttf
-monospaced.1.5.family=DejaVu Serif
-serif.3.7.file=/usr/share/fonts/truetype/dejavu/DejaVuSans-Bold.ttf
-serif.0.8.family=DejaVu Sans
-monospaced.0.4.file=/usr/share/fonts/truetype/dejavu/DejaVuSerif-Bold.ttf
-monospaced.3.10.file=/usr/share/fonts/truetype/dejavu/DejaVuSans.ttf
-serif.1.1.family=DejaVu Serif
-sansserif.2.1.file=/usr/share/fonts/truetype/dejavu/DejaVuSans-BoldOblique.ttf
-sansserif.1.6.file=/usr/share/fonts/truetype/dejavu/DejaVuSansMono.ttf
-monospaced.2.8.family=DejaVu Serif
-sansserif.3.2.family=DejaVu Sans
-monospaced.1.3.file=/usr/share/fonts/truetype/dejavu/DejaVuSerif-Bold.ttf
-monospaced.3.1.family=DejaVu Sans Mono
-monospaced.0.8.file=/usr/share/fonts/truetype/dejavu/DejaVuSans-BoldOblique.ttf
-sansserif.3.0.file=/usr/share/fonts/truetype/dejavu/DejaVuSans-BoldOblique.ttf
-serif.3.4.family=DejaVu Sans
-sansserif.2.5.file=/usr/share/fonts/truetype/dejavu/DejaVuSerif-BoldItalic.ttf
-sansserif.3.length=9
-serif.0.5.family=DejaVu Sans Mono
-monospaced.2.2.file=/usr/share/fonts/truetype/dejavu/DejaVuSerif-Italic.ttf
-monospaced.1.7.file=/usr/share/fonts/truetype/dejavu/DejaVuSans-BoldOblique.ttf
-sansserif.3.4.file=/usr/share/fonts/truetype/dejavu/DejaVuSerif-BoldItalic.ttf
-sansserif.2.6.family=DejaVu Sans Mono
-monospaced.3.1.file=/usr/share/fonts/truetype/dejavu/DejaVuSansMono-Oblique.ttf
-monospaced.2.5.family=DejaVu Sans
-serif.1.8.family=DejaVu Sans
-monospaced.2.6.file=/usr/share/fonts/truetype/dejavu/DejaVuSans.ttf
-monospaced.3.10.family=DejaVu Sans
-serif.2.1.family=DejaVu Serif
-sansserif.0.0.file=/usr/share/fonts/truetype/dejavu/DejaVuSans.ttf
-sansserif.0.0.family=DejaVu Sans
-sansserif.3.8.file=/usr/share/fonts/truetype/dejavu/DejaVuSansMono.ttf
-serif.0.3.file=/usr/share/fonts/truetype/dejavu/DejaVuSerif-BoldItalic.ttf
-monospaced.3.8.family=DejaVu Sans
-monospaced.3.5.file=/usr/share/fonts/truetype/dejavu/DejaVuSerif-Italic.ttf
-sansserif.1.3.family=DejaVu Sans
-serif.1.2.file=/usr/share/fonts/truetype/dejavu/DejaVuSerif-BoldItalic.ttf
-sansserif.0.4.file=/usr/share/fonts/truetype/dejavu/DejaVuSansMono.ttf
-monospaced.1.2.family=DejaVu Sans
-serif.0.7.file=/usr/share/fonts/truetype/dejavu/DejaVuSans-Oblique.ttf
-serif.1.5.family=DejaVu Sans Mono
-monospaced.3.9.file=/usr/share/fonts/truetype/dejavu/DejaVuSerif-Bold.ttf
-serif.2.1.file=/usr/share/fonts/truetype/dejavu/DejaVuSerif-BoldItalic.ttf
-sansserif.3.6.family=DejaVu Sans Mono
-serif.1.6.file=/usr/share/fonts/truetype/dejavu/DejaVuSans.ttf
-sansserif.0.8.file=/usr/share/fonts/truetype/dejavu/DejaVuSerif-BoldItalic.ttf
diff --git a/tests/test_integration_workflow/input_files/synthetic.mate_1.bed b/tests/test_integration_workflow/input_files/synthetic.mate_1.bed
index f838343e902d43817f8d2dabd7c82b7c62a5f755..47335f6a30c2f03477886531c57f6408d2ae391b 100644
--- a/tests/test_integration_workflow/input_files/synthetic.mate_1.bed
+++ b/tests/test_integration_workflow/input_files/synthetic.mate_1.bed
@@ -1,10 +1,10 @@
-1-10000-20000	3397	3472	NS500318:863:HY2KYBGXC:1:11101:14671:1067	0	+	DDX11L1
-1-10000-20000	3249	3324	NS500318:863:HY2KYBGXC:1:11101:24439:1068	0	+	DDX11L1
-1-10000-20000	3735	3810	NS500318:863:HY2KYBGXC:1:11101:14965:1069	0	+	DDX11L1
-1-10000-20000	2055	2130	NS500318:863:HY2KYBGXC:1:11101:21081:1069	0	+	DDX11L1
-1-10000-20000	3567	3642	NS500318:863:HY2KYBGXC:1:11101:18197:1070	0	+	DDX11L1
-1-10000-20000	7920	7995	NS500318:863:HY2KYBGXC:1:11101:4614:1071	0	-	WASH7P
-1-10000-20000	6665	6740	NS500318:863:HY2KYBGXC:1:11101:8467:1073	0	-	WASH7P
-1-10000-20000	6915	6990	NS500318:863:HY2KYBGXC:1:11101:18960:1076	0	-	WASH7P
-1-10000-20000	5841	5916	NS500318:863:HY2KYBGXC:1:11101:6851:1076	0	-	WASH7P
-1-10000-20000	7929	8004	NS500318:863:HY2KYBGXC:1:11101:14731:1078	0	-	WASH7P
+1-10000-20000	3397	3472	NS500318:863:HY2KYBGXC:1:11101:14671:1067	0	+	ENSG00000223972
+1-10000-20000	3249	3324	NS500318:863:HY2KYBGXC:1:11101:24439:1068	0	+	ENSG00000223972
+1-10000-20000	3735	3810	NS500318:863:HY2KYBGXC:1:11101:14965:1069	0	+	ENSG00000223972
+1-10000-20000	2055	2130	NS500318:863:HY2KYBGXC:1:11101:21081:1069	0	+	ENSG00000223972
+1-10000-20000	3567	3642	NS500318:863:HY2KYBGXC:1:11101:18197:1070	0	+	ENSG00000223972
+1-10000-20000	7945	8020	NS500318:863:HY2KYBGXC:1:11101:4614:1071	0	-	ENSG00000227232
+1-10000-20000	6690	6765	NS500318:863:HY2KYBGXC:1:11101:8467:1073	0	-	ENSG00000227232
+1-10000-20000	6940	7015	NS500318:863:HY2KYBGXC:1:11101:18960:1076	0	-	ENSG00000227232
+1-10000-20000	5866	5941	NS500318:863:HY2KYBGXC:1:11101:6851:1076	0	-	ENSG00000227232
+1-10000-20000	7954	8029	NS500318:863:HY2KYBGXC:1:11101:14731:1078	0	-	ENSG00000227232
diff --git a/tests/test_integration_workflow/input_files/synthetic.mate_2.bed b/tests/test_integration_workflow/input_files/synthetic.mate_2.bed
index de4b7133d0fa866c071cdd8d31e522bee5e30bf4..7e09a2d4998b30d045850887089957f08cc1c6f3 100644
--- a/tests/test_integration_workflow/input_files/synthetic.mate_2.bed
+++ b/tests/test_integration_workflow/input_files/synthetic.mate_2.bed
@@ -1,10 +1,10 @@
-1-10000-20000	3422	3497	NS500318:863:HY2KYBGXC:1:11101:14671:1067	0	+	DDX11L1
-1-10000-20000	3274	3349	NS500318:863:HY2KYBGXC:1:11101:24439:1068	0	+	DDX11L1
-1-10000-20000	3760	3835	NS500318:863:HY2KYBGXC:1:11101:14965:1069	0	+	DDX11L1
-1-10000-20000	2080	2155	NS500318:863:HY2KYBGXC:1:11101:21081:1069	0	+	DDX11L1
-1-10000-20000	3592	3667	NS500318:863:HY2KYBGXC:1:11101:18197:1070	0	+	DDX11L1
-1-10000-20000	7945	8020	NS500318:863:HY2KYBGXC:1:11101:4614:1071	0	-	WASH7P
-1-10000-20000	6690	6765	NS500318:863:HY2KYBGXC:1:11101:8467:1073	0	-	WASH7P
-1-10000-20000	6940	7015	NS500318:863:HY2KYBGXC:1:11101:18960:1076	0	-	WASH7P
-1-10000-20000	5866	5941	NS500318:863:HY2KYBGXC:1:11101:6851:1076	0	-	WASH7P
-1-10000-20000	7954	8029	NS500318:863:HY2KYBGXC:1:11101:14731:1078	0	-	WASH7P
+1-10000-20000	3422	3497	NS500318:863:HY2KYBGXC:1:11101:14671:1067	0	+	ENSG00000223972
+1-10000-20000	3274	3349	NS500318:863:HY2KYBGXC:1:11101:24439:1068	0	+	ENSG00000223972
+1-10000-20000	3760	3835	NS500318:863:HY2KYBGXC:1:11101:14965:1069	0	+	ENSG00000223972
+1-10000-20000	2080	2155	NS500318:863:HY2KYBGXC:1:11101:21081:1069	0	+	ENSG00000223972
+1-10000-20000	3592	3667	NS500318:863:HY2KYBGXC:1:11101:18197:1070	0	+	ENSG00000223972
+1-10000-20000	7920	7995	NS500318:863:HY2KYBGXC:1:11101:4614:1071	0	-	ENSG00000227232
+1-10000-20000	6665	6740	NS500318:863:HY2KYBGXC:1:11101:8467:1073	0	-	ENSG00000227232
+1-10000-20000	6915	6990	NS500318:863:HY2KYBGXC:1:11101:18960:1076	0	-	ENSG00000227232
+1-10000-20000	5841	5916	NS500318:863:HY2KYBGXC:1:11101:6851:1076	0	-	ENSG00000227232
+1-10000-20000	7929	8004	NS500318:863:HY2KYBGXC:1:11101:14731:1078	0	-	ENSG00000227232
diff --git a/tests/test_integration_workflow/input_files/synthetic.paired.bed b/tests/test_integration_workflow/input_files/synthetic.paired.bed
deleted file mode 100644
index e372afbf8082916f55425f7cd333fac0da908d55..0000000000000000000000000000000000000000
--- a/tests/test_integration_workflow/input_files/synthetic.paired.bed
+++ /dev/null
@@ -1,10 +0,0 @@
-1-10000-20000	3397	3497	NS500318:863:HY2KYBGXC:1:11101:14671:1067	0	+	DDX11L1
-1-10000-20000	3249	3349	NS500318:863:HY2KYBGXC:1:11101:24439:1068	0	+	DDX11L1
-1-10000-20000	3735	3835	NS500318:863:HY2KYBGXC:1:11101:14965:1069	0	+	DDX11L1
-1-10000-20000	2055	2155	NS500318:863:HY2KYBGXC:1:11101:21081:1069	0	+	DDX11L1
-1-10000-20000	3567	3667	NS500318:863:HY2KYBGXC:1:11101:18197:1070	0	+	DDX11L1
-1-10000-20000	7920	8020	NS500318:863:HY2KYBGXC:1:11101:4614:1071	0	-	WASH7P
-1-10000-20000	6665	6765	NS500318:863:HY2KYBGXC:1:11101:8467:1073	0	-	WASH7P
-1-10000-20000	6915	7015	NS500318:863:HY2KYBGXC:1:11101:18960:1076	0	-	WASH7P
-1-10000-20000	5841	5941	NS500318:863:HY2KYBGXC:1:11101:6851:1076	0	-	WASH7P
-1-10000-20000	7929	8029	NS500318:863:HY2KYBGXC:1:11101:14731:1078	0	-	WASH7P
diff --git a/tests/test_integration_workflow/test.local.sh b/tests/test_integration_workflow/test.local.sh
index 6bcf8d68dabf4492282ed9b039b4387c758cadbb..ac753e8d274908e9dc298d86b958b923417656c6 100755
--- a/tests/test_integration_workflow/test.local.sh
+++ b/tests/test_integration_workflow/test.local.sh
@@ -1,7 +1,8 @@
 #!/bin/bash
 
 # Tear down test environment
-trap 'rm -rf logs/ results/ .snakemake/ && cd $user_dir' EXIT  # quoted command is exected after script exits, regardless of exit status
+#trap 'rm -rf logs/ results/ .snakemake/ && cd $user_dir' EXIT  # quoted command is exected after script exits, regardless of exit status
+trap 'cd $user_dir' EXIT  # quoted command is exected after script exits, regardless of exit status
 
 # Set up test environment
 set -eo pipefail  # ensures that script exits at first command that exits with non-zero status
@@ -21,6 +22,8 @@ snakemake \
     --rerun-incomplete \
     --use-singularity \
     --singularity-args="--bind ${PWD}"
+
+# Check md5 sum of some output files
 find results/ -type f -name \*\.gz -exec gunzip '{}' \;
 find results/ -type f -name \*\.zip -exec sh -c 'unzip -o {} -d $(dirname {})' \;
 md5sum --check "expected_output.md5"
@@ -36,3 +39,45 @@ md5sum --check "expected_output.md5"
 #     -exec sh -c 'unzip -o {} -d $(dirname {})' \;
 # md5sum $(cat expected_output.files) > expected_output.md5
 
+# Check whether STAR produces expected alignments
+# STAR alignments need to be fully within ground truth alignments for tests to pass; not checking 
+# vice versa because processing might cut off parts of reads (if testing STAR directly, add '-f 1' 
+# as additional option)
+echo "Verifying STAR output"
+result=$(bedtools intersect -F 1 -v -bed \
+    -a input_files/synthetic.mate_1.bed \
+    -b results/single_end/synthetic_10_reads_mate_1/map_genome/synthetic_10_reads_mate_1_Aligned.sortedByCoord.out.bam \
+    | wc -l)
+if [ $result != "0" ]; then
+    echo "Alignments for mate 1 reads are not consistent with ground truth"
+    exit 1
+fi
+result=$(bedtools intersect -F 1 -v -bed \
+    -a input_files/synthetic.mate_2.bed \
+    -b results/single_end/synthetic_10_reads_mate_2/map_genome/synthetic_10_reads_mate_2_Aligned.sortedByCoord.out.bam \
+    | wc -l)
+if [ $result != "0" ]; then
+    echo "Alignments for mate 1 reads are not consistent with ground truth"
+    exit 1
+fi
+result=$(bedtools intersect -F 1 -v -bed \
+    -a <(cat input_files/synthetic.mate_1.bed input_files/synthetic.mate_2.bed) \
+    -b results/paired_end/synthetic_10_reads_paired/map_genome/synthetic_10_reads_paired_Aligned.sortedByCoord.out.bam \
+    | wc -l)
+if [ $result != "0" ]; then
+    echo "Alignments for mate 1 reads are not consistent with ground truth"
+    exit 1
+fi
+
+# Check whether Salmon assigns reads to expected genes
+echo "Verifying Salmon output"
+diff \
+    <(cat results/single_end/synthetic_10_reads_mate_1/salmon_quant/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \
+    <(cat input_files/synthetic.mate_1.bed | cut -f7 | sort | uniq -c | sort -k2nr | awk '{printf($2"\t"$1"\n")}')
+diff \
+    <(cat results/single_end/synthetic_10_reads_mate_2/salmon_quant/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \
+    <(cat input_files/synthetic.mate_2.bed | cut -f7 | sort | uniq -c | sort -k2nr | awk '{printf($2"\t"$1"\n")}')
+diff \
+    <(cat results/paired_end/synthetic_10_reads_paired/salmon_quant/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \
+    <(cat input_files/synthetic.mate_1.bed | cut -f7 | sort | uniq -c | sort -k2nr | awk '{printf($2"\t"$1"\n")}')
+
diff --git a/tests/test_integration_workflow/test.slurm.sh b/tests/test_integration_workflow/test.slurm.sh
index efa55a3f02d24f4128d4479bf9e3ff304a33dd1e..2f2c9e76c307383f31bae337dc3b88b573c356d2 100755
--- a/tests/test_integration_workflow/test.slurm.sh
+++ b/tests/test_integration_workflow/test.slurm.sh
@@ -39,3 +39,45 @@ md5sum --check "expected_output.md5"
 #     -exec sh -c 'unzip -o {} -d $(dirname {})' \;
 # md5sum $(cat expected_output.files) > expected_output.md5
 
+# Check whether STAR produces expected alignments
+# STAR alignments need to be fully within ground truth alignments for tests to pass; not checking 
+# vice versa because processing might cut off parts of reads (if testing STAR directly, add '-f 1' 
+# as additional option)
+echo "Verifying STAR output"
+result=$(bedtools intersect -F 1 -v -bed \
+    -a input_files/synthetic.mate_1.bed \
+    -b results/single_end/synthetic_10_reads_mate_1/map_genome/synthetic_10_reads_mate_1_Aligned.sortedByCoord.out.bam \
+    | wc -l)
+if [ $result != "0" ]; then
+    echo "Alignments for mate 1 reads are not consistent with ground truth"
+    exit 1
+fi
+result=$(bedtools intersect -F 1 -v -bed \
+    -a input_files/synthetic.mate_2.bed \
+    -b results/single_end/synthetic_10_reads_mate_2/map_genome/synthetic_10_reads_mate_2_Aligned.sortedByCoord.out.bam \
+    | wc -l)
+if [ $result != "0" ]; then
+    echo "Alignments for mate 1 reads are not consistent with ground truth"
+    exit 1
+fi
+result=$(bedtools intersect -F 1 -v -bed \
+    -a <(cat input_files/synthetic.mate_1.bed input_files/synthetic.mate_2.bed) \
+    -b results/paired_end/synthetic_10_reads_paired/map_genome/synthetic_10_reads_paired_Aligned.sortedByCoord.out.bam \
+    | wc -l)
+if [ $result != "0" ]; then
+    echo "Alignments for mate 1 reads are not consistent with ground truth"
+    exit 1
+fi
+
+# Check whether Salmon assigns reads to expected genes
+echo "Verifying Salmon output"
+diff \
+    <(cat results/single_end/synthetic_10_reads_mate_1/salmon_quant/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \
+    <(cat input_files/synthetic.mate_1.bed | cut -f7 | sort | uniq -c | sort -k2nr | awk '{printf($2"\t"$1"\n")}')
+diff \
+    <(cat results/single_end/synthetic_10_reads_mate_2/salmon_quant/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \
+    <(cat input_files/synthetic.mate_2.bed | cut -f7 | sort | uniq -c | sort -k2nr | awk '{printf($2"\t"$1"\n")}')
+diff \
+    <(cat results/paired_end/synthetic_10_reads_paired/salmon_quant/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \
+    <(cat input_files/synthetic.mate_1.bed | cut -f7 | sort | uniq -c | sort -k2nr | awk '{printf($2"\t"$1"\n")}')
+