diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 4d4f4c3abd6b184555bf3609481240cfa86c1c22..43321795ef74fd293cab88baace30000bec42220 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -5,10 +5,11 @@ before_script:
test:
script:
+ # add code quality tests here
+ # add unit tests here
+ # add script tests here
- bash tests/test_scripts_labkey_to_snakemake/test.sh
- - cd snakemake # fix this in future version; all tests
- - snakemake -n # should be called from home directory
- - bash run_test.sh #
- - cd .. #
- # add additional tests here
+ # add integration tests here
+ - bash tests/test_create_dag_chart/test.sh
+ - bash tests/test_integration_workflow/test.local.sh
diff --git a/images/workflow_dag.svg b/images/workflow_dag.svg
new file mode 100644
index 0000000000000000000000000000000000000000..0a20c622abd4ecc5445ca54416183cc3e5dc9557
--- /dev/null
+++ b/images/workflow_dag.svg
@@ -0,0 +1,95 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
+ "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
+<!-- Generated by graphviz version 2.42.3 (20191010.1750)
+ -->
+<!-- Title: snakemake_dag Pages: 1 -->
+<svg width="699pt" height="188pt"
+ viewBox="0.00 0.00 699.00 188.00" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
+<g id="graph0" class="graph" transform="scale(1 1) rotate(0) translate(4 184)">
+<title>snakemake_dag</title>
+<polygon fill="white" stroke="transparent" points="-4,4 -4,-184 695,-184 695,4 -4,4"/>
+<!-- 0 -->
+<g id="node1" class="node">
+<title>0</title>
+<path fill="none" stroke="#d88d56" stroke-width="2" d="M357.5,-36C357.5,-36 327.5,-36 327.5,-36 321.5,-36 315.5,-30 315.5,-24 315.5,-24 315.5,-12 315.5,-12 315.5,-6 321.5,0 327.5,0 327.5,0 357.5,0 357.5,0 363.5,0 369.5,-6 369.5,-12 369.5,-12 369.5,-24 369.5,-24 369.5,-30 363.5,-36 357.5,-36"/>
+<text text-anchor="middle" x="342.5" y="-15.5" font-family="sans" font-size="10.00">finish</text>
+</g>
+<!-- 1 -->
+<g id="node2" class="node">
+<title>1</title>
+<path fill="none" stroke="#56d873" stroke-width="2" d="M155,-108C155,-108 12,-108 12,-108 6,-108 0,-102 0,-96 0,-96 0,-84 0,-84 0,-78 6,-72 12,-72 12,-72 155,-72 155,-72 161,-72 167,-78 167,-84 167,-84 167,-96 167,-96 167,-102 161,-108 155,-108"/>
+<text text-anchor="middle" x="83.5" y="-93" font-family="sans" font-size="10.00">pe_fastqc</text>
+<text text-anchor="middle" x="83.5" y="-82" font-family="sans" font-size="10.00">sample: HNRNPC_control_rep1</text>
+</g>
+<!-- 1->0 -->
+<g id="edge1" class="edge">
+<title>1->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M146.53,-71.97C196.33,-58.51 264.12,-40.18 305.52,-29"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="306.45,-32.37 315.19,-26.38 304.63,-25.61 306.45,-32.37"/>
+</g>
+<!-- 2 -->
+<g id="node3" class="node">
+<title>2</title>
+<path fill="none" stroke="#56d873" stroke-width="2" d="M320,-108C320,-108 197,-108 197,-108 191,-108 185,-102 185,-96 185,-96 185,-84 185,-84 185,-78 191,-72 197,-72 197,-72 320,-72 320,-72 326,-72 332,-78 332,-84 332,-84 332,-96 332,-96 332,-102 326,-108 320,-108"/>
+<text text-anchor="middle" x="258.5" y="-93" font-family="sans" font-size="10.00">pe_fastqc</text>
+<text text-anchor="middle" x="258.5" y="-82" font-family="sans" font-size="10.00">sample: HNRNPC_KD_rep1</text>
+</g>
+<!-- 2->0 -->
+<g id="edge2" class="edge">
+<title>2->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M279.26,-71.7C289.74,-62.97 302.61,-52.24 314,-42.75"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="316.53,-45.19 321.97,-36.1 312.05,-39.82 316.53,-45.19"/>
+</g>
+<!-- 3 -->
+<g id="node4" class="node">
+<title>3</title>
+<path fill="none" stroke="#afd856" stroke-width="2" d="M490.5,-108C490.5,-108 362.5,-108 362.5,-108 356.5,-108 350.5,-102 350.5,-96 350.5,-96 350.5,-84 350.5,-84 350.5,-78 356.5,-72 362.5,-72 362.5,-72 490.5,-72 490.5,-72 496.5,-72 502.5,-78 502.5,-84 502.5,-84 502.5,-96 502.5,-96 502.5,-102 496.5,-108 490.5,-108"/>
+<text text-anchor="middle" x="426.5" y="-87.5" font-family="sans" font-size="10.00">pe_remove_polya_cutadapt</text>
+</g>
+<!-- 3->0 -->
+<g id="edge3" class="edge">
+<title>3->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M405.74,-71.7C395.26,-62.97 382.39,-52.24 371,-42.75"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="372.95,-39.82 363.03,-36.1 368.47,-45.19 372.95,-39.82"/>
+</g>
+<!-- 4 -->
+<g id="node5" class="node">
+<title>4</title>
+<path fill="none" stroke="#afd856" stroke-width="2" d="M667.5,-108C667.5,-108 539.5,-108 539.5,-108 533.5,-108 527.5,-102 527.5,-96 527.5,-96 527.5,-84 527.5,-84 527.5,-78 533.5,-72 539.5,-72 539.5,-72 667.5,-72 667.5,-72 673.5,-72 679.5,-78 679.5,-84 679.5,-84 679.5,-96 679.5,-96 679.5,-102 673.5,-108 667.5,-108"/>
+<text text-anchor="middle" x="603.5" y="-87.5" font-family="sans" font-size="10.00">pe_remove_polya_cutadapt</text>
+</g>
+<!-- 4->0 -->
+<g id="edge4" class="edge">
+<title>4->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M539.99,-71.97C489.66,-58.47 421.11,-40.08 379.42,-28.9"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="380.25,-25.5 369.69,-26.29 378.44,-32.26 380.25,-25.5"/>
+</g>
+<!-- 5 -->
+<g id="node6" class="node">
+<title>5</title>
+<path fill="none" stroke="#5692d8" stroke-width="2" d="M494,-180C494,-180 351,-180 351,-180 345,-180 339,-174 339,-168 339,-168 339,-156 339,-156 339,-150 345,-144 351,-144 351,-144 494,-144 494,-144 500,-144 506,-150 506,-156 506,-156 506,-168 506,-168 506,-174 500,-180 494,-180"/>
+<text text-anchor="middle" x="422.5" y="-165" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text>
+<text text-anchor="middle" x="422.5" y="-154" font-family="sans" font-size="10.00">sample: HNRNPC_control_rep1</text>
+</g>
+<!-- 5->3 -->
+<g id="edge5" class="edge">
+<title>5->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M423.49,-143.7C423.93,-135.98 424.46,-126.71 424.95,-118.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="428.45,-118.29 425.52,-108.1 421.46,-117.89 428.45,-118.29"/>
+</g>
+<!-- 6 -->
+<g id="node7" class="node">
+<title>6</title>
+<path fill="none" stroke="#5692d8" stroke-width="2" d="M679,-180C679,-180 536,-180 536,-180 530,-180 524,-174 524,-168 524,-168 524,-156 524,-156 524,-150 530,-144 536,-144 536,-144 679,-144 679,-144 685,-144 691,-150 691,-156 691,-156 691,-168 691,-168 691,-174 685,-180 679,-180"/>
+<text text-anchor="middle" x="607.5" y="-165" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text>
+<text text-anchor="middle" x="607.5" y="-154" font-family="sans" font-size="10.00">sample: HNRNPC_KD_rep1</text>
+</g>
+<!-- 6->4 -->
+<g id="edge6" class="edge">
+<title>6->4</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M606.51,-143.7C606.07,-135.98 605.54,-126.71 605.05,-118.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="608.54,-117.89 604.48,-108.1 601.55,-118.29 608.54,-117.89"/>
+</g>
+</g>
+</svg>
diff --git a/scripts/labkey_api.py b/scripts/labkey_api.py
old mode 100644
new mode 100755
diff --git a/snakemake/create_snakemake_flowchart.sh b/snakemake/create_snakemake_flowchart.sh
deleted file mode 100755
index ce71a9a3dcfcd940c55d9568bff4e10bfa670f45..0000000000000000000000000000000000000000
--- a/snakemake/create_snakemake_flowchart.sh
+++ /dev/null
@@ -1 +0,0 @@
-snakemake --dag -np | dot -Tpng > dag.png
diff --git a/snakemake/run_snakefile.sh b/snakemake/run_snakefile.sh
deleted file mode 100755
index ceec8a8493b661eab1c279a7e44a6f82d2d77ba6..0000000000000000000000000000000000000000
--- a/snakemake/run_snakefile.sh
+++ /dev/null
@@ -1,13 +0,0 @@
-# set -e
-
-mkdir -p logs/cluster_log
-mkdir -p logs/local_log
-
-snakemake \
---cluster-config cluster.json \
---cluster "sbatch --cpus-per-task={cluster.threads} --mem={cluster.mem} --qos={cluster.queue} --time={cluster.time} --job-name={cluster.name} -o {cluster.out} -p scicore" \
---cores 256 \
--p \
---rerun-incomplete \
---use-singularity \
---singularity-args "--bind ${PWD}"
diff --git a/snakemake/run_test.sh b/snakemake/run_test.sh
deleted file mode 100755
index 2569ff03ade35606ca8f2afde9a66e791c349377..0000000000000000000000000000000000000000
--- a/snakemake/run_test.sh
+++ /dev/null
@@ -1,11 +0,0 @@
-# set -e
-
-mkdir -p logs/cluster_log
-mkdir -p logs/local_log
-
-snakemake \
---cores 4 \
--p \
---rerun-incomplete \
---use-singularity \
---singularity-args "--bind ${PWD}/../tests/input_files"
diff --git a/tests/samples.tsv b/tests/samples.tsv
deleted file mode 100644
index 76687a52bfe23a9bcbbba3e36ad54cdefb68afe4..0000000000000000000000000000000000000000
--- a/tests/samples.tsv
+++ /dev/null
@@ -1,3 +0,0 @@
-sample fq1 fq2 fq1_3p fq1_5p fq2_3p fq2_5p fq1_polya fq2_polya organism index_size multimappers soft_clip pass_mode gtf_filtered libtype kallisto_directionality mean sd genome gtf tr_fasta_filtered kmer seqmode
-HNRNPC_control_rep1 ../tests/input_files/GSM1502498_1.fastq.gz ../tests/input_files/GSM1502498_2.fastq.gz AGATCGGAAGAGCACA XXXXXXXX AGATCGGAAGAGCGT XXXXXXXX AAAAAAAAAAAAAAAAAAAA TTTTTTTTTTTTTTTTTTT homo_sapiens 100 10 Local Basic ../tests/input_files/Homo_sapiens.GRCh38.99.chr.chrom_22.gtf A kallisto_directionality 250 100 ../tests/input_files/Homo_sapiens.GRCh38.dna_sm.primary_assembly.chrom_22.fa ../tests/input_files/Homo_sapiens.GRCh38.99.chr.chrom_22.gtf ../tests/input_files/transcripts_chrom_22.fa 31 fr
-HNRNPC_KD_rep1 ../tests/input_files/GSM1502500_1.fastq.gz ../tests/input_files/GSM1502500_2.fastq.gz AGATCGGAAGAGCACA XXXXXXXX AGATCGGAAGAGCGT XXXXXXXX AAAAAAAAAAAAAAAAAAAA TTTTTTTTTTTTTTTTTTT homo_sapiens 100 10 Local Basic ../tests/input_files/Homo_sapiens.GRCh38.99.chr.filterd.chrom_22.gtf A kallisto_directionality 250 100 ../tests/input_files/Homo_sapiens.GRCh38.dna_sm.primary_assembly.chrom_22.fa ../tests/input_files/Homo_sapiens.GRCh38.99.chr.chrom_22.gtf ../tests/input_files/transcripts_chrom_22.fa 31 fr
diff --git a/tests/test_create_dag_chart/.snakemake/log/2020-02-04T153123.241756.snakemake.log b/tests/test_create_dag_chart/.snakemake/log/2020-02-04T153123.241756.snakemake.log
new file mode 100644
index 0000000000000000000000000000000000000000..7cc0fe8473c4827e78d992d089f98d315ffdb3fa
--- /dev/null
+++ b/tests/test_create_dag_chart/.snakemake/log/2020-02-04T153123.241756.snakemake.log
@@ -0,0 +1,9 @@
+FileNotFoundError in line 13 of /scicore/home/zavolan/kanitz/SANDBOX/rnaseqpipeline/snakemake/Snakefile:
+[Errno 2] No such file or directory: 'input_files/samples.tsv'
+ File "/scicore/home/zavolan/kanitz/SANDBOX/rnaseqpipeline/snakemake/Snakefile", line 13, in <module>
+ File "/scicore/home/zavolan/kanitz/REMOVE_FROM_HOME/soft/miniconda3/envs/rnaseq_pipeline/lib/python3.6/site-packages/pandas/io/parsers.py", line 676, in parser_f
+ File "/scicore/home/zavolan/kanitz/REMOVE_FROM_HOME/soft/miniconda3/envs/rnaseq_pipeline/lib/python3.6/site-packages/pandas/io/parsers.py", line 448, in _read
+ File "/scicore/home/zavolan/kanitz/REMOVE_FROM_HOME/soft/miniconda3/envs/rnaseq_pipeline/lib/python3.6/site-packages/pandas/io/parsers.py", line 880, in __init__
+ File "/scicore/home/zavolan/kanitz/REMOVE_FROM_HOME/soft/miniconda3/envs/rnaseq_pipeline/lib/python3.6/site-packages/pandas/io/parsers.py", line 1126, in _make_engine
+ File "/scicore/home/zavolan/kanitz/REMOVE_FROM_HOME/soft/miniconda3/envs/rnaseq_pipeline/lib/python3.6/site-packages/pandas/io/parsers.py", line 2269, in __init__
+ File "/scicore/home/zavolan/kanitz/REMOVE_FROM_HOME/soft/miniconda3/envs/rnaseq_pipeline/lib/python3.6/site-packages/pandas/io/common.py", line 431, in get_handle
diff --git a/tests/test_create_dag_chart/.snakemake/log/2020-02-04T153204.024195.snakemake.log b/tests/test_create_dag_chart/.snakemake/log/2020-02-04T153204.024195.snakemake.log
new file mode 100644
index 0000000000000000000000000000000000000000..898b19839a9429523c3aed8b34cea0e74cc13acf
--- /dev/null
+++ b/tests/test_create_dag_chart/.snakemake/log/2020-02-04T153204.024195.snakemake.log
@@ -0,0 +1,5 @@
+Building DAG of jobs...
+MissingInputException in line 2 of /scicore/home/zavolan/kanitz/SANDBOX/rnaseqpipeline/snakemake/paired_end.snakefile:
+Missing input files for rule pe_fastqc:
+input_files/GSM1502498_1.fastq.gz
+input_files/GSM1502498_2.fastq.gz
diff --git a/tests/test_create_dag_chart/.snakemake/log/2020-02-04T153253.153466.snakemake.log b/tests/test_create_dag_chart/.snakemake/log/2020-02-04T153253.153466.snakemake.log
new file mode 100644
index 0000000000000000000000000000000000000000..0c88f192e934e1e40caab68b69ae031337a87490
--- /dev/null
+++ b/tests/test_create_dag_chart/.snakemake/log/2020-02-04T153253.153466.snakemake.log
@@ -0,0 +1,5 @@
+Building DAG of jobs...
+MissingInputException in line 2 of /scicore/home/zavolan/kanitz/SANDBOX/rnaseqpipeline/snakemake/paired_end.snakefile:
+Missing input files for rule pe_fastqc:
+input_files/GSM1502500_1.fastq.gz
+input_files/GSM1502500_2.fastq.gz
diff --git a/tests/test_create_dag_chart/.snakemake/log/2020-02-04T153305.441930.snakemake.log b/tests/test_create_dag_chart/.snakemake/log/2020-02-04T153305.441930.snakemake.log
new file mode 100644
index 0000000000000000000000000000000000000000..1c497506158408d785d63a482e84434c03d065d2
--- /dev/null
+++ b/tests/test_create_dag_chart/.snakemake/log/2020-02-04T153305.441930.snakemake.log
@@ -0,0 +1 @@
+Building DAG of jobs...
diff --git a/tests/test_create_dag_chart/.snakemake/log/2020-02-04T153343.033762.snakemake.log b/tests/test_create_dag_chart/.snakemake/log/2020-02-04T153343.033762.snakemake.log
new file mode 100644
index 0000000000000000000000000000000000000000..1c497506158408d785d63a482e84434c03d065d2
--- /dev/null
+++ b/tests/test_create_dag_chart/.snakemake/log/2020-02-04T153343.033762.snakemake.log
@@ -0,0 +1 @@
+Building DAG of jobs...
diff --git a/tests/test_create_dag_chart/.snakemake/log/2020-02-04T153536.300877.snakemake.log b/tests/test_create_dag_chart/.snakemake/log/2020-02-04T153536.300877.snakemake.log
new file mode 100644
index 0000000000000000000000000000000000000000..1c497506158408d785d63a482e84434c03d065d2
--- /dev/null
+++ b/tests/test_create_dag_chart/.snakemake/log/2020-02-04T153536.300877.snakemake.log
@@ -0,0 +1 @@
+Building DAG of jobs...
diff --git a/tests/test_create_dag_chart/.snakemake/log/2020-02-04T154438.496145.snakemake.log b/tests/test_create_dag_chart/.snakemake/log/2020-02-04T154438.496145.snakemake.log
new file mode 100644
index 0000000000000000000000000000000000000000..1c497506158408d785d63a482e84434c03d065d2
--- /dev/null
+++ b/tests/test_create_dag_chart/.snakemake/log/2020-02-04T154438.496145.snakemake.log
@@ -0,0 +1 @@
+Building DAG of jobs...
diff --git a/snakemake/config.yaml b/tests/test_create_dag_chart/config.yaml
similarity index 92%
rename from snakemake/config.yaml
rename to tests/test_create_dag_chart/config.yaml
index 80641a90cd98c6df1421965406defd27a1d84a81..dade873fec556edaf954f8cb72d7d4b39097eb81 100644
--- a/snakemake/config.yaml
+++ b/tests/test_create_dag_chart/config.yaml
@@ -13,7 +13,7 @@
##############################################################################
### Output and log directories
##############################################################################
- database_path: "/scicore/home/zavolan/GROUP/Rna_Seq_pipeline/Blabla"
+ database_path: "/some/path"
STAR_idx_folder: "STAR_indices"
output_dir: "results"
star_indexes: "results"
@@ -25,5 +25,5 @@
##############################################################################
### Sample info
##############################################################################
- samples: "../tests/samples.tsv"
+ samples: "input_files/samples.tsv"
...
diff --git a/tests/input_files/GSM1502498_1.fastq.gz b/tests/test_create_dag_chart/input_files/GSM1502498_1.fastq.gz
similarity index 100%
rename from tests/input_files/GSM1502498_1.fastq.gz
rename to tests/test_create_dag_chart/input_files/GSM1502498_1.fastq.gz
diff --git a/tests/input_files/GSM1502498_2.fastq.gz b/tests/test_create_dag_chart/input_files/GSM1502498_2.fastq.gz
similarity index 100%
rename from tests/input_files/GSM1502498_2.fastq.gz
rename to tests/test_create_dag_chart/input_files/GSM1502498_2.fastq.gz
diff --git a/tests/input_files/GSM1502500_1.fastq.gz b/tests/test_create_dag_chart/input_files/GSM1502500_1.fastq.gz
similarity index 100%
rename from tests/input_files/GSM1502500_1.fastq.gz
rename to tests/test_create_dag_chart/input_files/GSM1502500_1.fastq.gz
diff --git a/tests/input_files/GSM1502500_2.fastq.gz b/tests/test_create_dag_chart/input_files/GSM1502500_2.fastq.gz
similarity index 100%
rename from tests/input_files/GSM1502500_2.fastq.gz
rename to tests/test_create_dag_chart/input_files/GSM1502500_2.fastq.gz
diff --git a/tests/test_create_dag_chart/input_files/samples.tsv b/tests/test_create_dag_chart/input_files/samples.tsv
new file mode 100644
index 0000000000000000000000000000000000000000..3b68b12a51e433d2a44c6d100ccdcd7f84275347
--- /dev/null
+++ b/tests/test_create_dag_chart/input_files/samples.tsv
@@ -0,0 +1,3 @@
+sample fq1 fq2 fq1_3p fq1_5p fq2_3p fq2_5p fq1_polya fq2_polya organism index_size multimappers soft_clip pass_mode gtf_filtered libtype kallisto_directionality mean sd genome gtf tr_fasta_filtered kmer seqmode
+HNRNPC_control_rep1 input_files/GSM1502498_1.fastq.gz input_files/GSM1502498_2.fastq.gz AGATCGGAAGAGCACA XXXXXXXX AGATCGGAAGAGCGT XXXXXXXX AAAAAAAAAAAAAAAAAAAA TTTTTTTTTTTTTTTTTTT homo_sapiens 100 10 Local Basic input_files/Homo_sapiens.GRCh38.99.chr.chrom_22.gtf A kallisto_directionality 250 100 input_files/Homo_sapiens.GRCh38.dna_sm.primary_assembly.chrom_22.fa input_files/Homo_sapiens.GRCh38.99.chr.chrom_22.gtf input_files/transcripts_chrom_22.fa 31 fr
+HNRNPC_KD_rep1 input_files/GSM1502500_1.fastq.gz input_files/GSM1502500_2.fastq.gz AGATCGGAAGAGCACA XXXXXXXX AGATCGGAAGAGCGT XXXXXXXX AAAAAAAAAAAAAAAAAAAA TTTTTTTTTTTTTTTTTTT homo_sapiens 100 10 Local Basic input_files/Homo_sapiens.GRCh38.99.chr.filterd.chrom_22.gtf A kallisto_directionality 250 100 input_files/Homo_sapiens.GRCh38.dna_sm.primary_assembly.chrom_22.fa input_files/Homo_sapiens.GRCh38.99.chr.chrom_22.gtf input_files/transcripts_chrom_22.fa 31 fr
diff --git a/tests/test_create_dag_chart/test.sh b/tests/test_create_dag_chart/test.sh
new file mode 100755
index 0000000000000000000000000000000000000000..5ae27d01be3638ab78a259d0650c418b55c497d4
--- /dev/null
+++ b/tests/test_create_dag_chart/test.sh
@@ -0,0 +1,22 @@
+#!/bin/bash
+
+# Tear down test environment
+trap 'cd $user_dir' EXIT # quotes command is exected after script exits, regardless of exit status
+
+# Set up test environment
+set -eo pipefail # ensures that script exits at first command that exits with non-zero status
+set -u # ensures that script exits when unset variables are used
+set -x # facilitates debugging by printing out executed commands
+user_dir=$PWD
+script_dir="$(cd "$(dirname "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd)"
+cd $script_dir
+
+# Run tests
+snakemake \
+ --snakefile="../../snakemake/Snakefile" \
+ --configfile="config.yaml" \
+ --dag \
+ --printshellcmds \
+ --dryrun \
+ | dot -Tsvg > "../../images/workflow_dag.svg"
+
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
new file mode 100644
index 0000000000000000000000000000000000000000..270b359742115fa3a7f00c42493a5359aa9a4787
--- /dev/null
+++ 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
@@ -0,0 +1,245 @@
+#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
new file mode 100644
index 0000000000000000000000000000000000000000..dd359b621e3e83ecf601dd2891099e85cb555ce8
--- /dev/null
+++ 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
@@ -0,0 +1,245 @@
+#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
+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
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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
new file mode 100644
index 0000000000000000000000000000000000000000..20526159a6869e870fdc7fd1ce299f942b776c4f
--- /dev/null
+++ 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
@@ -0,0 +1,245 @@
+#JDK Font Configuration Generated File: *Do Not Edit*
+#Tue Feb 04 12:10:34 UTC 2020
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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
new file mode 100644
index 0000000000000000000000000000000000000000..7605aed3c618c5309bd1877221a773ff7938770c
--- /dev/null
+++ 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
@@ -0,0 +1,245 @@
+#JDK Font Configuration Generated File: *Do Not Edit*
+#Tue Feb 04 12:10:35 UTC 2020
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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
new file mode 100644
index 0000000000000000000000000000000000000000..207503ef9ae7a90077a9d6b18352b4889edecb22
--- /dev/null
+++ 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
@@ -0,0 +1,245 @@
+#JDK Font Configuration Generated File: *Do Not Edit*
+#Tue Feb 04 12:05:16 UTC 2020
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+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/snakemake/cluster.json b/tests/test_integration_workflow/cluster.json
similarity index 100%
rename from snakemake/cluster.json
rename to tests/test_integration_workflow/cluster.json
diff --git a/tests/test_integration_workflow/config.yaml b/tests/test_integration_workflow/config.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..dade873fec556edaf954f8cb72d7d4b39097eb81
--- /dev/null
+++ b/tests/test_integration_workflow/config.yaml
@@ -0,0 +1,29 @@
+---
+ ##############################################################################
+ ### Annotation
+ ##############################################################################
+ organism: "Homo_sapiens"
+ annotation: "../prepare_annotation/results/annotation.gtf"
+ genome: "../prepare_annotation/results/genome.fa"
+ annotation_filtered: "../prepare_annotation/results/filtered_transcripts.gtf"
+ STAR_index: "../prepare_annotation/results/STAR_index/"
+ other_RNAs_sequence: "../prepare_annotation/other.fa"
+ other_RNAs_index: "../prepare_annotation/results/other_RNAs_sequence.idx"
+ salmon_index: "../prepare_annotation/results/filtered_transcripts_salmon.idx/"
+ ##############################################################################
+ ### Output and log directories
+ ##############################################################################
+ database_path: "/some/path"
+ STAR_idx_folder: "STAR_indices"
+ output_dir: "results"
+ star_indexes: "results"
+ salmon_indexes: "results"
+ kallisto_indexes: "results"
+ local_log: "logs/local_log"
+ cluster_log: "logs/cluster_log"
+
+ ##############################################################################
+ ### Sample info
+ ##############################################################################
+ samples: "input_files/samples.tsv"
+...
diff --git a/tests/test_integration_workflow/expected_output.md5 b/tests/test_integration_workflow/expected_output.md5
new file mode 100644
index 0000000000000000000000000000000000000000..15304472f9bce85c14955250fdd93c113e7fa32c
--- /dev/null
+++ b/tests/test_integration_workflow/expected_output.md5
@@ -0,0 +1,12 @@
+c45be0333e4d84285d530855342763e0 results/paired_end/HNRNPC_control_rep1/HNRNPC_control_rep1.remove_adapters_mate1.fastq
+e1e0d16add8db1a314c780d497e863c9 results/paired_end/HNRNPC_control_rep1/HNRNPC_control_rep1.remove_polya_mate2.fastq
+7c63754abeff36d37b4d32c15d603e93 results/paired_end/HNRNPC_control_rep1/mate1_fastqc/GSM1502498_1_fastqc.html
+a46359f784d3eca4268c788a74789bf2 results/paired_end/HNRNPC_control_rep1/HNRNPC_control_rep1.remove_polya_mate1.fastq
+58ef63f61c82e050f05b871eea8d4b25 results/paired_end/HNRNPC_control_rep1/HNRNPC_control_rep1.remove_adapters_mate2.fastq
+794e0ed5b9abdeba17627ca76a298001 results/paired_end/HNRNPC_control_rep1/mate2_fastqc/GSM1502498_2_fastqc.html
+d3898e6e03d98db65b61172f8275f319 results/paired_end/HNRNPC_KD_rep1/HNRNPC_KD_rep1.remove_adapters_mate2.fastq
+e4eb9fe5f364c6f3395fc678b80853f9 results/paired_end/HNRNPC_KD_rep1/mate1_fastqc/GSM1502500_1_fastqc.html
+489e5a5bd92fafe9a79e164fb334e036 results/paired_end/HNRNPC_KD_rep1/HNRNPC_KD_rep1.remove_polya_mate2.fastq
+8a01f7aa476992c2bc32d3457f703865 results/paired_end/HNRNPC_KD_rep1/HNRNPC_KD_rep1.remove_adapters_mate1.fastq
+befd24fe0de9a24c853eb3c29d175168 results/paired_end/HNRNPC_KD_rep1/mate2_fastqc/GSM1502500_2_fastqc.html
+f048f50b6695c80e2c9d4ecf10c0d0a9 results/paired_end/HNRNPC_KD_rep1/HNRNPC_KD_rep1.remove_polya_mate1.fastq
diff --git a/tests/test_integration_workflow/input_files/GSM1502498_1.fastq.gz b/tests/test_integration_workflow/input_files/GSM1502498_1.fastq.gz
new file mode 100644
index 0000000000000000000000000000000000000000..f0f809c910078827ae704dc48fcb74591e17d115
Binary files /dev/null and b/tests/test_integration_workflow/input_files/GSM1502498_1.fastq.gz differ
diff --git a/tests/test_integration_workflow/input_files/GSM1502498_2.fastq.gz b/tests/test_integration_workflow/input_files/GSM1502498_2.fastq.gz
new file mode 100644
index 0000000000000000000000000000000000000000..e2b4bf1100444d1cf7a635b82d443ef6f43eb065
Binary files /dev/null and b/tests/test_integration_workflow/input_files/GSM1502498_2.fastq.gz differ
diff --git a/tests/test_integration_workflow/input_files/GSM1502500_1.fastq.gz b/tests/test_integration_workflow/input_files/GSM1502500_1.fastq.gz
new file mode 100644
index 0000000000000000000000000000000000000000..875d4dc285ac03883e8daa541660bfe0abacbb54
Binary files /dev/null and b/tests/test_integration_workflow/input_files/GSM1502500_1.fastq.gz differ
diff --git a/tests/test_integration_workflow/input_files/GSM1502500_2.fastq.gz b/tests/test_integration_workflow/input_files/GSM1502500_2.fastq.gz
new file mode 100644
index 0000000000000000000000000000000000000000..baddedb840b4a4dece8d352af4c779dc05aa5311
Binary files /dev/null and b/tests/test_integration_workflow/input_files/GSM1502500_2.fastq.gz differ
diff --git a/tests/input_files/Homo_sapiens.GRCh38.99.chr.chrom_22.gtf b/tests/test_integration_workflow/input_files/Homo_sapiens.GRCh38.99.chr.chrom_22.gtf
similarity index 100%
rename from tests/input_files/Homo_sapiens.GRCh38.99.chr.chrom_22.gtf
rename to tests/test_integration_workflow/input_files/Homo_sapiens.GRCh38.99.chr.chrom_22.gtf
diff --git a/tests/input_files/Homo_sapiens.GRCh38.dna_sm.primary_assembly.chrom_22.fa b/tests/test_integration_workflow/input_files/Homo_sapiens.GRCh38.dna_sm.primary_assembly.chrom_22.fa
similarity index 100%
rename from tests/input_files/Homo_sapiens.GRCh38.dna_sm.primary_assembly.chrom_22.fa
rename to tests/test_integration_workflow/input_files/Homo_sapiens.GRCh38.dna_sm.primary_assembly.chrom_22.fa
diff --git a/tests/test_integration_workflow/input_files/samples.tsv b/tests/test_integration_workflow/input_files/samples.tsv
new file mode 100644
index 0000000000000000000000000000000000000000..3b68b12a51e433d2a44c6d100ccdcd7f84275347
--- /dev/null
+++ b/tests/test_integration_workflow/input_files/samples.tsv
@@ -0,0 +1,3 @@
+sample fq1 fq2 fq1_3p fq1_5p fq2_3p fq2_5p fq1_polya fq2_polya organism index_size multimappers soft_clip pass_mode gtf_filtered libtype kallisto_directionality mean sd genome gtf tr_fasta_filtered kmer seqmode
+HNRNPC_control_rep1 input_files/GSM1502498_1.fastq.gz input_files/GSM1502498_2.fastq.gz AGATCGGAAGAGCACA XXXXXXXX AGATCGGAAGAGCGT XXXXXXXX AAAAAAAAAAAAAAAAAAAA TTTTTTTTTTTTTTTTTTT homo_sapiens 100 10 Local Basic input_files/Homo_sapiens.GRCh38.99.chr.chrom_22.gtf A kallisto_directionality 250 100 input_files/Homo_sapiens.GRCh38.dna_sm.primary_assembly.chrom_22.fa input_files/Homo_sapiens.GRCh38.99.chr.chrom_22.gtf input_files/transcripts_chrom_22.fa 31 fr
+HNRNPC_KD_rep1 input_files/GSM1502500_1.fastq.gz input_files/GSM1502500_2.fastq.gz AGATCGGAAGAGCACA XXXXXXXX AGATCGGAAGAGCGT XXXXXXXX AAAAAAAAAAAAAAAAAAAA TTTTTTTTTTTTTTTTTTT homo_sapiens 100 10 Local Basic input_files/Homo_sapiens.GRCh38.99.chr.filterd.chrom_22.gtf A kallisto_directionality 250 100 input_files/Homo_sapiens.GRCh38.dna_sm.primary_assembly.chrom_22.fa input_files/Homo_sapiens.GRCh38.99.chr.chrom_22.gtf input_files/transcripts_chrom_22.fa 31 fr
diff --git a/tests/input_files/transcripts_chrom_22.fa b/tests/test_integration_workflow/input_files/transcripts_chrom_22.fa
similarity index 100%
rename from tests/input_files/transcripts_chrom_22.fa
rename to tests/test_integration_workflow/input_files/transcripts_chrom_22.fa
diff --git a/tests/test_integration_workflow/test.local.sh b/tests/test_integration_workflow/test.local.sh
new file mode 100755
index 0000000000000000000000000000000000000000..926b70c0caaa9ce015c2cfb06838c25a5feef7d5
--- /dev/null
+++ b/tests/test_integration_workflow/test.local.sh
@@ -0,0 +1,38 @@
+#!/bin/bash
+
+# Tear down test environment
+trap 'rm -rf logs/ results/ .snakemake/ && cd $user_dir' EXIT # quotes command is exected after script exits, regardless of exit status
+
+# Set up test environment
+set -eo pipefail # ensures that script exits at first command that exits with non-zero status
+set -u # ensures that script exits when unset variables are used
+set -x # facilitates debugging by printing out executed commands
+user_dir=$PWD
+script_dir="$(cd "$(dirname "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd)"
+cd $script_dir
+mkdir -p logs/local_log
+
+# Run tests
+snakemake \
+ --snakefile="../../snakemake/Snakefile" \
+ --configfile="config.yaml" \
+ --cores=4 \
+ --printshellcmds \
+ --rerun-incomplete \
+ --use-singularity \
+ --singularity-args "--bind ${PWD}"
+find results/ -type f -name \*\.gz -exec gunzip '{}' \;
+md5sum --check "expected_output.md5"
+
+# Checksum file generated with
+# find results/ \
+# -type f \
+# -name \*\.gz \
+# -exec gunzip '{}' \;
+# find results/ \
+# -type f \
+# -regextype posix-egrep \
+# -regex ".*\.(fastq|html)$" \
+# -exec md5sum '{}' \; \
+# > expected_output.md5
+
diff --git a/tests/test_integration_workflow/test.slurm.sh b/tests/test_integration_workflow/test.slurm.sh
new file mode 100755
index 0000000000000000000000000000000000000000..719d1fd7bc7fe8afcad5decdc36e2815cfc2b03e
--- /dev/null
+++ b/tests/test_integration_workflow/test.slurm.sh
@@ -0,0 +1,41 @@
+#!/bin/bash
+
+# Tear down test environment
+trap 'rm -rf logs/ results/ .snakemake/ && cd $user_dir' EXIT # quotes command is exected after script exits, regardless of exit status
+
+# Set up test environment
+set -eo pipefail # ensures that script exits at first command that exits with non-zero status
+set -u # ensures that script exits when unset variables are used
+set -x # facilitates debugging by printing out executed commands
+user_dir=$PWD
+script_dir="$(cd "$(dirname "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd)"
+cd $script_dir
+mkdir -p logs/cluster_log
+mkdir -p logs/local_log
+
+# Run tests
+snakemake \
+ --snakefile="../../snakemake/Snakefile" \
+ --configfile="config.yaml" \
+ --cluster-config="cluster.json" \
+ --cluster="sbatch --cpus-per-task={cluster.threads} --mem={cluster.mem} --qos={cluster.queue} --time={cluster.time} --job-name={cluster.name} -o {cluster.out} -p scicore" \
+ --cores=256 \
+ --printshellcmds \
+ --rerun-incomplete \
+ --use-singularity \
+ --singularity-args "--bind ${PWD}"
+find results/ -type f -name \*\.gz -exec gunzip '{}' \;
+md5sum --check "expected_output.md5"
+
+# Checksum file generated with
+# find results/ \
+# -type f \
+# -name \*\.gz \
+# -exec gunzip '{}' \;
+# find results/ \
+# -type f \
+# -regextype posix-egrep \
+# -regex ".*\.(fastq|html)$" \
+# -exec md5sum '{}' \; \
+# > expected_output.md5
+