From b59bc7369056261726dec559eee7585b54692084 Mon Sep 17 00:00:00 2001
From: Pieter Neerincx <pieter.neerincx@gmail.com>
Date: Mon, 19 Jun 2023 20:50:58 +0200
Subject: [PATCH 01/42] Improved indentation check.

---
 check/indentationcheck.sh | 12 ++----------
 1 file changed, 2 insertions(+), 10 deletions(-)

diff --git a/check/indentationcheck.sh b/check/indentationcheck.sh
index 76d9536..61af252 100755
--- a/check/indentationcheck.sh
+++ b/check/indentationcheck.sh
@@ -1,19 +1,11 @@
 #!/bin/bash
 
-#
-# Use either WORKSPACE location for Jenkins or
-# resolve path to scripts we need to check
-# when executed manually outside Jenkins.
-#
-if [[ -z "${WORKSPACE:-}" ]]; then
-	MYDIR="$(cd -P "$(dirname "${0}")" && pwd)"
-	WORKSPACE="$(dirname ${MYDIR})"
-fi
+MYDIR="$(cd -P "$(dirname "${0}")" && pwd)"
 
 echo '#####################################################################################'
 echo '  Bash code must be indented with TABs. Checking for lines indented with spaces ... '
 echo '#####################################################################################'
-grep -n '^[[:space:]]* [[:space:]]*' "${WORKSPACE:-../}/protocols/"*.sh
+grep --recursive --line-number --include='*.*sh' --exclude-dir='deprecated' '^[[:space:]]* [[:space:]]*' "${MYDIR}"/../
 grep_exit_status="${?}"
 if [[ "${grep_exit_status}" -eq 0 ]]; then
 	echo '#####################################################################################'

From 8baa99c01c3e170110406ef0caf4bdea1fb4edb6 Mon Sep 17 00:00:00 2001
From: Pieter Neerincx <pieter.neerincx@gmail.com>
Date: Mon, 19 Jun 2023 21:01:47 +0200
Subject: [PATCH 02/42] Added .gitattributes and .gitignore

---
 .gitattributes | 6 ++++++
 .gitignore     | 5 +++++
 2 files changed, 11 insertions(+)
 create mode 100644 .gitattributes
 create mode 100644 .gitignore

diff --git a/.gitattributes b/.gitattributes
new file mode 100644
index 0000000..b161dc8
--- /dev/null
+++ b/.gitattributes
@@ -0,0 +1,6 @@
+* text=auto
+
+*.sh        eol=lf
+*.bash      eol=lf
+*.md        eol=lf
+*.cfg       eol=lf
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..4acf491
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,5 @@
+*.DS_Store
+*.project
+*.pydevproject
+*.settings
+*.md.html
\ No newline at end of file

From a89528e3454e78b1a48c215cfdb55c907e0fba06 Mon Sep 17 00:00:00 2001
From: Pieter Neerincx <pieter.neerincx@gmail.com>
Date: Mon, 19 Jun 2023 21:02:05 +0200
Subject: [PATCH 03/42] Deleted .DS_Store

---
 .DS_Store | Bin 6148 -> 0 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)
 delete mode 100644 .DS_Store

diff --git a/.DS_Store b/.DS_Store
deleted file mode 100644
index b88e62a16ec5834473e782f6419d82132dd27833..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 6148
zcmeHKOHRW;41I<oTCwSp<y?UqL{&Kf7XZ>C5J5pr*=NVKdHxhJin3(^wq(B<k3EyT
z#dr)rHXpkiU=3hNRm7*7spz`uM9#vqAd2nr`m`I`$G-0-v2za1y+Dg+>}jj~72a_`
zk0Z6Eb{J0E^E6yyp!<Lqh8^pr6&-uLaiPP5jjPPLZ%KbLkPIXP$v`sj9~jUoN?Bex
zrcDNtfn?yD0lgmzRj~;i9qsC%u@-=+&v+A#t(PDcbr74t(UBgCcq-9TC0Y#eboxug
zHG!j}r$eIokT_YQLlHZj`xgs`G>&PLfn=a&;M}Kct^c>wnf|{{%2_gy4E!kuWU;;5
zZum=4TPHuKwYE_2sV8Bqh0|CmCR!=xL`(7YkGP^^t~Y_Bqovbt>BM{pC@(3=z;7_{
E1q2l+mjD0&


From c2c0fb25f1cd5de41fb4a5e883646b2574f3a543 Mon Sep 17 00:00:00 2001
From: Pieter Neerincx <pieter.neerincx@gmail.com>
Date: Mon, 19 Jun 2023 21:03:28 +0200
Subject: [PATCH 04/42] Fixed indentation and some shellcheck issues in
 scripts.

---
 checkEnvironment.sh                | 20 ++++++++++----------
 templates/generate_template.sh     |  4 ++--
 test/autotest_generate_template.sh |  6 +++---
 test/protocols/Autotest.sh         | 10 +++++-----
 4 files changed, 20 insertions(+), 20 deletions(-)

diff --git a/checkEnvironment.sh b/checkEnvironment.sh
index 1d85f64..f05d6d2 100755
--- a/checkEnvironment.sh
+++ b/checkEnvironment.sh
@@ -1,6 +1,6 @@
 HOST=$1
 
-if [ -f ./environment_checks.txt ]
+if [[ -f ./environment_checks.txt ]]
 then
 	rm ./environment_checks.txt
 fi
@@ -10,29 +10,29 @@ TMPDIR=""
 GROUP=""
 if [ "${HOST}" == "zinc-finger.gcc.rug.nl" ]
 then
-    	ENVIRONMENT_PARAMETERS="zinc-finger"
-        TMPDIR="tmp05"
+	ENVIRONMENT_PARAMETERS="zinc-finger"
+	TMPDIR="tmp05"
 elif [ "${HOST}" == "leucine-zipper.gcc.rug.nl" ]
 then
-    	ENVIRONMENT_PARAMETERS="leucine-zipper"
-        TMPDIR="tmp06"
+	ENVIRONMENT_PARAMETERS="leucine-zipper"
+	TMPDIR="tmp06"
 elif [ "${HOST}" == "calculon" ]
 then
-    	ENVIRONMENT_PARAMETERS="calculon"
-        TMPDIR="tmp04"
+	ENVIRONMENT_PARAMETERS="calculon"
+	TMPDIR="tmp04"
 else
-    	echo "unknown host: running is only possible on calculon,zinc-finger or leucine-zipper"
+	echo "Unknown host: running is only possible on calculon, zinc-finger or leucine-zipper."
 fi
 
 THISDIR=$(pwd)
 if [[ $THISDIR == *"/groups/umcg-gaf/"* ]]
 then
 	GROUP="umcg-gaf" 
-elif [[ $THISDIR == *"/groups/umcg-gd/"* ]] 
+elif [[ $THISDIR == *"/groups/umcg-gd/"* ]]
 then
 	GROUP="umcg-gd"
 else
-	echo "this is not a known group, please run only in umcg-gd or umcg-gaf group"
+	echo "This is not a known group. Please run only in umcg-gd or umcg-gaf group."
 fi
 
 printf "${ENVIRONMENT_PARAMETERS}\t${TMPDIR}\t${GROUP}" > ./environment_checks.txt
diff --git a/templates/generate_template.sh b/templates/generate_template.sh
index 7202b24..9bd28b6 100755
--- a/templates/generate_template.sh
+++ b/templates/generate_template.sh
@@ -5,7 +5,7 @@ then
 	echo "RNA pipeline loaded, proceeding"
 else
 	echo "No RNA pipeline loaded, exiting"
-        exit 1
+	exit 1
 fi
 
 module list
@@ -58,7 +58,7 @@ workflow="${EBROOTNGS_RNA}/workflow_${pipeline}.csv"
 
 if [ -f .compute.properties ];
 then
-     rm .compute.properties
+	rm .compute.properties
 fi
 
 perl "${EBROOTNGS_RNA}/convertParametersGitToMolgenis.pl" "${EBROOTNGS_RNA}/parameters.${species}.${build}.csv" > \
diff --git a/test/autotest_generate_template.sh b/test/autotest_generate_template.sh
index c8f714c..74f74f1 100755
--- a/test/autotest_generate_template.sh
+++ b/test/autotest_generate_template.sh
@@ -20,12 +20,12 @@ PIPELINE="hisat" # hisat, lexogen
 
 WORKFLOW=${EBROOTNGS_RNA}/test_workflow_${PIPELINE}.csv
 
-if [ -f .compute.properties ];
+if [[ -f .compute.properties ]]
 then
-     rm .compute.properties
+	rm .compute.properties
 fi
 
-if [ -f ${GAF}/generatedscripts/${PROJECT}/out.csv  ];
+if [[ -f ${GAF}/generatedscripts/${PROJECT}/out.csv ]]
 then
 	rm -rf ${GAF}/generatedscripts/${PROJECT}/out.csv
 fi
diff --git a/test/protocols/Autotest.sh b/test/protocols/Autotest.sh
index 3fb723e..d112f82 100755
--- a/test/protocols/Autotest.sh
+++ b/test/protocols/Autotest.sh
@@ -29,11 +29,11 @@ done
 
 if [[ -f "${testResults}/output_NGS_RNA/notInVcf1.txt" || -f "${testResults}/output_NGS_RNA/notInVcf2.txt" || -f "${testResults}/output_NGS_RNA/inconsistent.txt" || -f "${testResults}/output_NGS_RNA/"*.fail ]]
 then
-	echo "there are differences between the test and the original output"
-        echo "please fix the bug or update this test"
-        echo "the stats can be found here: ${testResults}/output_NGS_RNA/vcfStats.txt"
-        exit 1
+	echo "There are differences between the test and the original output."
+	echo "Please fix the bug or update this test."
+	echo "The stats can be found here: ${testResults}/output_NGS_RNA/vcfStats.txt"
+	exit 1
 else
-	echo "test succeeded"
+	echo "Test succeeded."
 	head -2 "${testResults}/output_NGS_RNA/vcfStats.txt"
 fi

From 2aa4be79b1fd0d68e49dd6d41da380e100aef18a Mon Sep 17 00:00:00 2001
From: gerbenvandervries <gerbenvandervries@gmail.com>
Date: Thu, 5 Jan 2023 14:11:05 +0000
Subject: [PATCH 05/42] typo

---
 test/test_pipeline.sh | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/test/test_pipeline.sh b/test/test_pipeline.sh
index 59745e8..982e9c2 100644
--- a/test/test_pipeline.sh
+++ b/test/test_pipeline.sh
@@ -6,7 +6,6 @@ function preparePipeline(){
 	local _projectName="PlatinumSubset_NGS_RNA"
 	local _generatedScriptsFolder="${workfolder}/generatedscripts/${_projectName}"
 
-	TMPHOME=/home/umcg-gvdvries/git/NGS_RNA
 	rm -f "${workfolder}/logs/${_projectName}/run01.pipeline.finished"
 	rsync -r --verbose --recursive --links --no-perms --times --group --no-owner --devices --specials "${pipelinefolder}/test/rawdata/MY_TEST_BAM_PROJECT/"SRR1552906[249]_[12].fq.gz "${workfolder}/rawdata/ngs/MY_TEST_BAM_PROJECT/"
 
@@ -56,7 +55,7 @@ function checkIfFinished(){
 	local _projectName="PlatinumSubset_NGS_RNA"
 	count=0
 	minutes=0
-	while [ ! -f "${workfolder}/projects/${_projectName}/run01/jobs/s15_Autotestt_0.sh.finished" ]
+	while [ ! -f "${workfolder}/projects/${_projectName}/run01/jobs/s15_Autotest_0.sh.finished" ]
 	do
 
 		echo "${_projectName} is not finished in $minutes minutes, sleeping for 2 minutes"

From 0d7a128d9e298b3cc276720f9f6a7984edc1390a Mon Sep 17 00:00:00 2001
From: gerbenvandervries <gerbenvandervries@gmail.com>
Date: Thu, 5 Jan 2023 14:58:53 +0000
Subject: [PATCH 06/42] trigger

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

diff --git a/README.md b/README.md
index 60a168b..6744355 100644
--- a/README.md
+++ b/README.md
@@ -1,4 +1,4 @@
-<h1> NGS_RNA pipeline</h1>
+<h1>NGS_RNA pipeline</h1>
 
 <h2>Description of the different steps used in the RNA analysis pipeline </h2>
 

From 68070f82968eac0819564edb8b2e5a14630a44e4 Mon Sep 17 00:00:00 2001
From: gerbenvandervries <gerbenvandervries@gmail.com>
Date: Thu, 5 Jan 2023 15:24:38 +0000
Subject: [PATCH 07/42] move resources

---
 parameters.homo_sapiens.GRCh37.csv | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/parameters.homo_sapiens.GRCh37.csv b/parameters.homo_sapiens.GRCh37.csv
index 557c216..b3b4dab 100755
--- a/parameters.homo_sapiens.GRCh37.csv
+++ b/parameters.homo_sapiens.GRCh37.csv
@@ -150,7 +150,7 @@ qcMatrics,${intermediateDir}/${externalSampleID}.total.qc.metrics.table
 ##### Protocols 3,6  (HTSeq count, MakeExpressionTable) #####
 sampleHTseqExpressionText,${intermediateDir}/${externalSampleID}.counts.txt
 projectHTseqExpressionTable,${intermediateDir}/${project}.expression.counts.table
-rnaSeQCGTF,/groups/umcg-solve-rd/tmp01/resources/GAD/gtf/gencode.v19.annotation.patched_contigs.genes.gtf
+rnaSeQCGTF,/apps/data/GAD/gtf/gencode.v19.annotation.patched_contigs.genes.gtf
 rnaSeQCDir,${projectResultsDir}/RNASeQC
 
 ##### GENOME,INDEX,ANNOTATION FILES #####

From be5189341d03e2654f7b1e625ceb5cd5bd589572 Mon Sep 17 00:00:00 2001
From: gerbenvandervries <gerbenvandervries@gmail.com>
Date: Fri, 6 Jan 2023 09:03:23 +0000
Subject: [PATCH 08/42] fix yaml config file fom MutliQC

---
 protocols/MultiQCReport.sh | 92 +++++++++++++++++++-------------------
 1 file changed, 46 insertions(+), 46 deletions(-)

diff --git a/protocols/MultiQCReport.sh b/protocols/MultiQCReport.sh
index 65e6ccd..37fdd48 100755
--- a/protocols/MultiQCReport.sh
+++ b/protocols/MultiQCReport.sh
@@ -38,52 +38,52 @@
 cat > "${intermediateDir}/${project}_QC_config.yaml" <<'_EOF'
 
 report_header_info:
-	- Contact E-mail: '${contact}'
-	- Pipeline Version: '${ngsVersion}'
-	- Project : '${project}'
-	- prepKit : '${prepKit}'
-	- '' : ''
-	- Used toolversions: ' '
-	- '' : ''
-	- '': ${jdkVersion}
-	- '': ${fastqcVersion}
-	- '': ${starVersion}
-	- '': ${samtoolsVersion}
-	- '': ${rVersion}
-	- '': ${wkhtmltopdfVersion}
-	- '': ${picardVersion}
-	- '': ${htseqVersion}
-	- '': ${pythonVersion}
-	- '': ${gatkVersion}
-	- '': ${multiqcVersion}
-	- '' : ''
-	- pipeline description : ''
-	- Gene expression quantification : ''
-	- '': 'The trimmed fastQ files where aligned to build ${indexFileID} reference genome using'
-	- '': '${starVersion} [1] allowing for 2 mismatches. Before gene quantification'
-	- '': '${samtoolsVersion} [2] was used to sort the aligned reads.'
-	- '': 'The gene level quantification was performed by ${htseqVersion} [3] using --mode=union'
-	- '': '--stranded=no and, Ensembl version 75 was used as gene annotation database which is included'
-	- '': 'in folder expression/.'
-	- '' : ''
-	- QC metrics: ''
-	- '': 'Quality control (QC) metrics are calculated for the raw sequencing data. This is done using'
-	- '': 'the tool FastQC FastQC [4]. QC metrics are calculated for the aligned reads using'
-	- '': 'Picard-tools [5] CollectRnaSeqMetrics, MarkDuplicates, CollectInsertSize-'
-	- '': 'Metrics and SAMtools flagstat.These QC metrics form the basis in this final QC report.'
-	- '' : ''
-	- references: ''
-	- '' : ''
-	- '': '1. Dobin A, Davis C a, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M,'
-	- '': 'Gingeras TR: STAR: ultrafast universal RNA-seq aligner. Bioinformatics 2013, 29:15–21.'
-	- '': '2. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R,'
-	- '': 'Subgroup 1000 Genome Project Data Processing: The Sequence Alignment/Map format and SAMtools.'
-	- '': 'Bioinforma 2009, 25 (16):2078–2079.'
-	- '': '3. Anders S, Pyl PT, Huber W: HTSeq – A Python framework to work with high-throughput sequencing data'
-	- '': 'HTSeq – A Python framework to work with high-throughput sequencing data. 2014:0–5.'
-	- '': '4. Andrews, S. (2010). FastQC a Quality Control Tool for High Throughput Sequence Data [Online].'
-	- '': 'Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ ${samtoolsVersion}'
-	- '': '5. Picard Sourceforge Web site. http://picard.sourceforge.net/ ${picardVersion}'
+  - 'Contact E-mail' : '${contact}'
+  - 'Pipeline Version' : '${ngsVersion}'
+  - 'Project' : '${project}'
+  - 'prepKit' : '${prepKit}'
+  - '' : ''
+  - 'Used toolversions' : ' '
+  - '' : ''
+  - '' : ${jdkVersion}
+  - '' : ${fastqcVersion}
+  - '' : ${starVersion}
+  - '' : ${samtoolsVersion}
+  - '' : ${rVersion}
+  - '' : ${wkhtmltopdfVersion}
+  - '' : ${picardVersion}
+  - '' : ${htseqVersion}
+  - '' : ${pythonVersion}
+  - '' : ${gatkVersion}
+  - '' : ${multiqcVersion}
+  - '' : ''
+  - 'pipeline description' : ''
+  - 'Gene expression quantification' : ''
+  - '' : 'The trimmed fastQ files where aligned to build ${indexFileID} reference genome using'
+  - '' : '${starVersion} [1] allowing for 2 mismatches. Before gene quantification'
+  - '' : '${samtoolsVersion} [2] was used to sort the aligned reads.'
+  - '' : 'The gene level quantification was performed by ${htseqVersion} [3] using --mode=union'
+  - '' : '--stranded=no and, Ensembl version 75 was used as gene annotation database which is included'
+  - '' : 'in folder expression/.'
+  - '' : ''
+  - 'QC metrics' : ''
+  - '' : 'Quality control (QC) metrics are calculated for the raw sequencing data. This is done using'
+  - '' : 'the tool FastQC FastQC [4]. QC metrics are calculated for the aligned reads using'
+  - '' : 'Picard-tools [5] CollectRnaSeqMetrics, MarkDuplicates, CollectInsertSize-'
+  - '' : 'Metrics and SAMtools flagstat.These QC metrics form the basis in this final QC report.'
+  - '' : ''
+  - 'references' : ''
+  - '' : ''
+  - '' : '1. Dobin A, Davis C a, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M,'
+  - '' : 'Gingeras TR: STAR: ultrafast universal RNA-seq aligner. Bioinformatics 2013, 29:15–21.'
+  - '' : '2. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R,'
+  - '' : 'Subgroup 1000 Genome Project Data Processing: The Sequence Alignment/Map format and SAMtools.'
+  - '' : 'Bioinforma 2009, 25 (16):2078–2079.'
+  - '' : '3. Anders S, Pyl PT, Huber W: HTSeq – A Python framework to work with high-throughput sequencing data'
+  - '' : 'HTSeq – A Python framework to work with high-throughput sequencing data. 2014:0–5.'
+  - '' : '4. Andrews, S. (2010). FastQC a Quality Control Tool for High Throughput Sequence Data [Online].'
+  - '' : 'Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ ${samtoolsVersion}'
+  - '' : '5. Picard Sourceforge Web site. http://picard.sourceforge.net/ ${picardVersion}'
 _EOF
 
 

From 4b54a5a8cd50227f0431703cbc4b12f4b0bbf78a Mon Sep 17 00:00:00 2001
From: gerbenvandervries <gerbenvandervries@gmail.com>
Date: Wed, 11 Jan 2023 13:20:03 +0100
Subject: [PATCH 09/42] remove failing date, and unneeded echo

---
 protocols/AddOrReplaceReadGroups.sh | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/protocols/AddOrReplaceReadGroups.sh b/protocols/AddOrReplaceReadGroups.sh
index bb38a1b..5fac966 100755
--- a/protocols/AddOrReplaceReadGroups.sh
+++ b/protocols/AddOrReplaceReadGroups.sh
@@ -32,7 +32,6 @@ module load "${picardVersion}"
 #check modules
 module list
 
-echo "## $(date) Start $0"
 
 java -Xmx6g -XX:ParallelGCThreads=8 -jar "${EBROOTPICARD}/${picardJar}" AddOrReplaceReadGroups \
 I="${sortedBam}" \
@@ -43,7 +42,6 @@ RGLB="${externalSampleID}" \
 RGPL=ILLUMINA \
 RGPU="${sequencer}_${flowcell}_${run}" \
 RGSM="${externalSampleID}" \
-RGDT=$(date --rfc-3339=date) \
 CREATE_INDEX=true \
 MAX_RECORDS_IN_RAM=4000000 \
 TMP_DIR="${tempDir}"
@@ -52,4 +50,3 @@ echo "returncode: $?";
 mv "${tmpAddOrReplaceGroupsBam}" "${addOrReplaceGroupsBam}"
 mv "${tmpAddOrReplaceGroupsBai}" "${addOrReplaceGroupsBai}"
 echo "succes moving files";
-echo "## $(date) ##  $0 Done "

From e7242f4afdd50537b58c9cdfa7c3a06bdcca9e8d Mon Sep 17 00:00:00 2001
From: gerbenvandervries <gerbenvandervries@gmail.com>
Date: Wed, 11 Jan 2023 13:20:52 +0100
Subject: [PATCH 10/42] shellcheck fixies

---
 protocols/BQSR.sh           | 13 ++-----------
 protocols/CombineFastq.sh   |  4 ++--
 protocols/CopyPrmTmpData.sh |  1 -
 3 files changed, 4 insertions(+), 14 deletions(-)

diff --git a/protocols/BQSR.sh b/protocols/BQSR.sh
index 3d1ba31..fa0b98c 100755
--- a/protocols/BQSR.sh
+++ b/protocols/BQSR.sh
@@ -27,23 +27,15 @@ makeTmpDir "${bqsrBai}"
 tmpBqsrBai=${MC_tmpFile}
 
 #Load Modules
-module load ${gatkVersion}
+module load "${gatkVersion}"
 
 #check modules
 module list
 
-echo "## $(date) Start $0"
-
-echo
-echo
 echo "Running GATK BQSR:"
 
 
-java -Dsamjdk.use_async_io_read_samtools=false \
--Dsamjdk.use_async_io_write_samtools=true \
--Dsamjdk.use_async_io_write_tribble=false \
--Dsamjdk.compression_level=2 \
--jar -Xmx7g -XX:ParallelGCThreads=2 -Djava.io.tmpdir="${tmpTmpDataDir}" \
+jan -jar -Xmx7g -XX:ParallelGCThreads=2 -Djava.io.tmpdir="${tmpTmpDataDir}" \
 "${EBROOTGATK}/gatk-package-4.1.4.1-local.jar" BaseRecalibrator \
 -R "${indexFile}" \
 -I "${splitAndTrimBam}" \
@@ -67,5 +59,4 @@ cd -
 
 echo "returncode: $?";
 echo "succes moving files";
-echo "## $(date) ##  $0 Done "
 
diff --git a/protocols/CombineFastq.sh b/protocols/CombineFastq.sh
index 7f52f32..e51eae0 100644
--- a/protocols/CombineFastq.sh
+++ b/protocols/CombineFastq.sh
@@ -40,12 +40,12 @@ INPUTSRIGHT=()
 
 for FqFileLeft in "${trimmedLeftBarcodeFqGz[@]}"
 do
-	array_contains INPUTSLEFT "${FqFileLeft}" || INPUTSLEFT+=("${FqFileLeft}")    # If bamFile does not exist in array add it
+	array_contains INPUTSLEFT "${FqFileLeft}" || INPUTSLEFT+=("${FqFileLeft}")
 done
 
 for FqFileRight in "${trimmedRightBarcodeFqGz[@]}"
 do
-	array_contains INPUTSRIGHT "${FqFileRight}" || INPUTSRIGHT+=("${FqFileRight}")    # If baiFile does not exist in array add it
+	array_contains INPUTSRIGHT "${FqFileRight}" || INPUTSRIGHT+=("${FqFileRight}")
 done
 
 if [[ "${#INPUTSLEFT[@]}" == 1 ]]
diff --git a/protocols/CopyPrmTmpData.sh b/protocols/CopyPrmTmpData.sh
index a325c70..d129791 100755
--- a/protocols/CopyPrmTmpData.sh
+++ b/protocols/CopyPrmTmpData.sh
@@ -21,7 +21,6 @@
 #list barcode
 #list lane
 
-n_elements="${internalSampleID[@]}"
 max_index="${#internalSampleID[@]}"-1
 
 for ((samplenumber = 0; samplenumber <= max_index; samplenumber++))

From 903621a804101b7186de06fc9ca9ff1d9b61f1bb Mon Sep 17 00:00:00 2001
From: gerbenvandervries <gerbenvandervries@gmail.com>
Date: Wed, 11 Jan 2023 15:02:23 +0100
Subject: [PATCH 11/42] shellcheck fixes

---
 protocols/BQSR.sh                             |  8 +--
 protocols/CombineFastq.sh                     |  4 +-
 protocols/CopyPrmTmpData.sh                   |  9 +--
 protocols/CopyToResultsDir.sh                 |  6 +-
 protocols/CreateExternSamplesProjects.sh      | 16 ++---
 protocols/CreateInhouseRnaSeqProjects.sh      | 22 +-----
 protocols/DE.sh                               |  6 +-
 protocols/Design.sh                           |  4 +-
 protocols/FastQC.sh                           | 22 +++---
 protocols/GatkGenotypeGvcf.sh                 | 30 ++++-----
 protocols/GatkHaplotypeCallerGvcf.sh          |  9 +--
 protocols/HTSeq_count.sh                      |  2 +-
 protocols/IndelRealignment.sh                 |  9 +--
 protocols/Leafcutter_intron_clustering.sh     |  4 +-
 protocols/MakeExpressionTable.sh              |  4 +-
 protocols/MarkDuplicates.sh                   |  8 +--
 protocols/MergeBam.sh                         | 20 +++---
 protocols/MultiQCReport.sh                    |  2 +-
 protocols/OUTRIDER.sh                         |  6 +-
 protocols/QCStats.sh                          | 67 +++++++++----------
 protocols/STAR.sh                             |  8 +--
 protocols/SplitAndTrim.sh                     | 12 +---
 protocols/Stranded.sh                         |  9 +--
 protocols/TIN.sh                              |  8 +--
 protocols/{ => deprecated}/GatkMergeGvcf.sh   | 12 ++--
 .../{ => deprecated}/filter_Leafcutter.sh     |  3 +-
 protocols/rMATs.sh                            |  2 +-
 27 files changed, 119 insertions(+), 193 deletions(-)
 rename protocols/{ => deprecated}/GatkMergeGvcf.sh (87%)
 rename protocols/{ => deprecated}/filter_Leafcutter.sh (93%)

diff --git a/protocols/BQSR.sh b/protocols/BQSR.sh
index fa0b98c..825aa1d 100755
--- a/protocols/BQSR.sh
+++ b/protocols/BQSR.sh
@@ -52,10 +52,10 @@ java -jar -Xmx7g -XX:ParallelGCThreads=2 -Djava.io.tmpdir="${tmpTmpDataDir}" \
 mv "${tmpBqsrBam}" "${bqsrBam}"
 mv "${tmpBqsrBai}" "${bqsrBai}"
 
-cd "${intermediateDir}"
-md5sum $(basename "${bqsrBam}")> $(basename "${bqsrBam}").md5
-md5sum $(basename "${bqsrBai}")> $(basename "${bqsrBai}").md5
-cd -
+cd "${intermediateDir}" || exit
+md5sum "$(basename "${bqsrBam}")" > "$(basename "${bqsrBam}").md5"
+md5sum "$(basename "${bqsrBai}")" > "$(basename "${bqsrBai}").md5"
+cd - || exit
 
 echo "returncode: $?";
 echo "succes moving files";
diff --git a/protocols/CombineFastq.sh b/protocols/CombineFastq.sh
index e51eae0..7817a2c 100644
--- a/protocols/CombineFastq.sh
+++ b/protocols/CombineFastq.sh
@@ -50,8 +50,8 @@ done
 
 if [[ "${#INPUTSLEFT[@]}" == 1 ]]
 then
-	ln -sf $(basename "${INPUTSLEFT[0]}") "${mergedLeftBarcodeFqGz}"
-	ln -sf $(basename "${INPUTSRIGHT[0]}") "${mergedRightBarcodeFqGz}"
+	ln -sf "$(basename "${INPUTSLEFT[0]}")" "${mergedLeftBarcodeFqGz}"
+	ln -sf "$(basename "${INPUTSRIGHT[0]}")" "${mergedRightBarcodeFqGz}"
 	echo "nothing to merge because there is only one sample"
 else
 	cat "${INPUTSLEFT[@]}" > "${tmpMergedLeftBarcodeFqGz}"
diff --git a/protocols/CopyPrmTmpData.sh b/protocols/CopyPrmTmpData.sh
index d129791..761a4bf 100755
--- a/protocols/CopyPrmTmpData.sh
+++ b/protocols/CopyPrmTmpData.sh
@@ -84,14 +84,11 @@ do
 
 done
 
-cd "${TMPDATADIR}"
-if md5sum -c *.md5 > "${RUNNAME}.md5.log" 2>&1
+cd "${TMPDATADIR}" || exit
+if md5sum -c ./*.md5 > "${RUNNAME}.md5.log" 2>&1
 then
 	echo 'PASS'
 else
 	echo 'FAILED'
 fi
-cd -
-
-
-
+cd - || exit
diff --git a/protocols/CopyToResultsDir.sh b/protocols/CopyToResultsDir.sh
index b08f186..7fa671e 100755
--- a/protocols/CopyToResultsDir.sh
+++ b/protocols/CopyToResultsDir.sh
@@ -61,8 +61,6 @@ mkdir -p "${projectResultsDir}/qcmetrics"
 
 # Copy BAM plus index plus md5 sum to results directory
 
-usedWorkflow=$(basename ${workflow})
-
 	rsync -avL "${intermediateDir}"/*.sorted.merged.bam "${projectResultsDir}/alignment/"
 	rsync -avL "${intermediateDir}"/*.sorted.merged.bam.{md5sum,bai,bai.md5sum} "${projectResultsDir}/alignment/"
 
@@ -79,7 +77,7 @@ usedWorkflow=$(basename ${workflow})
 	rsync -av "${intermediateDir}"/*.idxstats "${projectResultsDir}/qcmetrics/"
 	rsync -av "${intermediateDir}"/*.collectrnaseqmetrics "${projectResultsDir}/qcmetrics/"
 
-	if [ "${seqType}" == "PE" ]
+	if [[ "${seqType}" == "PE" ]]
 	then
 		rsync -av "${intermediateDir}"/*.insert_size_metrics "${projectResultsDir}/qcmetrics/"
 	else
@@ -112,7 +110,7 @@ usedWorkflow=$(basename ${workflow})
 # Copy STAR annotated SpliceJunctions
 	rsync -av "${intermediateDir}/"*.SJ.* "${projectResultsDir}/star_sj/"
 #only available with PE
-	if [ "${seqType}" == "PE" ]
+	if [[ "${seqType}" == "PE" ]]
 	then
 		rsync -av "${intermediateDir}"/*.insert_size_* "${projectResultsDir}/qcmetrics/"
 	else
diff --git a/protocols/CreateExternSamplesProjects.sh b/protocols/CreateExternSamplesProjects.sh
index 23f18d7..c22799c 100755
--- a/protocols/CreateExternSamplesProjects.sh
+++ b/protocols/CreateExternSamplesProjects.sh
@@ -30,10 +30,9 @@
 #list externalFastQ_1
 #list externalFastQ_2
 
-umask 0007
 module load "${ngsUtilsVersion}"
-
 module list
+
 #
 # Create project dirs.
 #
@@ -45,9 +44,9 @@ mkdir -p "${intermediateDir}"
 mkdir -p "${projectResultsDir}"
 mkdir -p "${projectQcDir}"
 
-ROCKETPOINT=`pwd`
+ROCKETPOINT="${PWD}"
 
-cd "${projectRawtmpDataDir}"
+cd "${projectRawtmpDataDir}" || exit
 
 #
 # Create symlinks to the raw data required to analyse this project
@@ -56,7 +55,6 @@ cd "${projectRawtmpDataDir}"
 #
 
 
-#n_elements="${internalSampleID[@]}"
 max_index="${#internalSampleID[@]}"-1
 for ((samplenumber = 0; samplenumber <= max_index; samplenumber++))
 do
@@ -87,16 +85,10 @@ do
 	fi
 done
 
-cd $ROCKETPOINT
+cd "${ROCKETPOINT}" || exit
 
-echo "before splitting"
-echo `pwd`
 module load "${ngsVersion}"
 
-#
-# TODO: array for each sample:
-#
-
 #
 # Create subset of samples for this project.
 #
diff --git a/protocols/CreateInhouseRnaSeqProjects.sh b/protocols/CreateInhouseRnaSeqProjects.sh
index 65abdfd..88dc334 100755
--- a/protocols/CreateInhouseRnaSeqProjects.sh
+++ b/protocols/CreateInhouseRnaSeqProjects.sh
@@ -32,12 +32,6 @@
 #list barcode
 #list lane
 
-#
-# Change permissions.
-#
-umask 0007
-
-#FIX!
 module load "${ngsVersion}"
 module load "${ngsUtilsVersion}"
 module list
@@ -53,9 +47,9 @@ mkdir -p "${intermediateDir}"
 mkdir -p "${projectResultsDir}"
 mkdir -p "${projectQcDir}"
 
-ROCKETPOINT=`pwd`
+ROCKETPOINT="${pwd}"
 
-cd "${projectRawtmpDataDir}"
+cd "${projectRawtmpDataDir}" || exit
 
 #
 # Create symlinks to the raw data required to analyse this project
@@ -63,7 +57,6 @@ cd "${projectRawtmpDataDir}"
 # For each sequence file (could be multiple per sample):
 #
 
-n_elements="${internalSampleID[@]}"
 max_index="${#internalSampleID[@]}-1"
 for ((samplenumber = 0; samplenumber <= max_index; samplenumber++))
 do
@@ -97,14 +90,8 @@ do
 done
 
 
-cd $ROCKETPOINT
+cd "${ROCKETPOINT}" || exit
 
-echo "before splitting"
-echo pwd
-
-#
-# TODO: array for each sample:
-#
 
 #
 # Create subset of samples for this project.
@@ -123,9 +110,6 @@ then
 	rm ../.compute.properties
 fi
 
-echo "before run second rocket"
-echo pwd
-
 sh "${EBROOTMOLGENISMINCOMPUTE}/molgenis_compute.sh" \
 -p "${mainParameters}" \
 -p "${parameters_build}" \
diff --git a/protocols/DE.sh b/protocols/DE.sh
index c4d271f..f0e0923 100755
--- a/protocols/DE.sh
+++ b/protocols/DE.sh
@@ -37,10 +37,10 @@ do
 	array_contains UNIQUESAMPLES "${sampleId}" || UNIQUESAMPLES+=("${sampleId}")    # If sampleId does not exist in array add it
 done
 
-cd "${intermediateDir}"
+cd "${intermediateDir}" || exit
 
 #detect number of conditions
-col=$(col="condition"; head -n1 "${projectJobsDir}/${project}.csv" | tr "," "\n" | grep -n $col)
+col=$(col="condition"; head -n1 "${projectJobsDir}/${project}.csv" | tr "," "\n" | grep -n "${col}")
 colArray=(${col//:/ })
 conditionCount=$(tail -n +2 "${projectJobsDir}/${project}.csv" | cut -d "," -f "${colArray[0]}" | sort | uniq | wc -l)
 
@@ -69,4 +69,4 @@ else
 	echo "running: deseq2 analysis"
 	Rscript "${EBROOTNGS_RNA}/scripts/deseq2_analysis.R" "${projectJobsDir}/${project}.csv" "${project}"
 fi
-cd -
+cd - || exit
diff --git a/protocols/Design.sh b/protocols/Design.sh
index b9536a0..ba33b14 100755
--- a/protocols/Design.sh
+++ b/protocols/Design.sh
@@ -35,7 +35,7 @@ do
 	array_contains UNIQUESAMPLES "${sample}" || UNIQUESAMPLES+=("${sample}")    # If bamFile does not exist in array add it
 done
 
-cd "${intermediateDir}"
+cd "${intermediateDir}" || exit
 
 #cleanup old file if present
 rm -f "${intermediateDir}/"*".design.tsv"
@@ -66,4 +66,4 @@ done
 
 echo "files written to: ${intermediateDir}/ *.design.tsv"
 
-cd -
+cd - || exit
diff --git a/protocols/FastQC.sh b/protocols/FastQC.sh
index a8d8204..509589f 100755
--- a/protocols/FastQC.sh
+++ b/protocols/FastQC.sh
@@ -21,26 +21,26 @@
 #string logsDir
 
 #Load module
-module load ${fastqcVersion}
+module load "${fastqcVersion}"
 module list
 
-makeTmpDir ${intermediateDir}
-tmpIntermediateDir=${MC_tmpFile}
+makeTmpDir "${intermediateDir}"
+tmpIntermediateDir="${MC_tmpFile}"
 
 #If paired-end do fastqc for both ends, else only for one
-if [ ${seqType} == "PE" ]
+if [[ "${seqType}" == "PE" ]]
 then
 	# end1 & end2
-	fastqc ${peEnd1BarcodeFqGz} \
-	${peEnd2BarcodeFqGz} \
-	-o ${tmpIntermediateDir}
+	fastqc "${peEnd1BarcodeFqGz}" \
+	"${peEnd2BarcodeFqGz}" \
+	-o "${tmpIntermediateDir}"
 
 	echo -e "\nFastQC finished succesfull. Moving temp files to final.\n\n"
-	mv -f ${tmpIntermediateDir}/* ${intermediateDir}
+	mv -f "${tmpIntermediateDir}/"* "${intermediateDir}"
 else
-	fastqc ${srBarcodeFqGz} \
-	-o ${tmpIntermediateDir}
+	fastqc "${srBarcodeFqGz}" \
+	-o "${tmpIntermediateDir}"
 	
 	echo -e "\nFastQC finished succesfull. Moving temp files to final.\n\n"
-	mv -f ${tmpIntermediateDir}/* ${intermediateDir}
+	mv -f "${tmpIntermediateDir}/"* "${intermediateDir}"
 fi
diff --git a/protocols/GatkGenotypeGvcf.sh b/protocols/GatkGenotypeGvcf.sh
index e00dbf9..19ad9f7 100755
--- a/protocols/GatkGenotypeGvcf.sh
+++ b/protocols/GatkGenotypeGvcf.sh
@@ -24,7 +24,7 @@ array_contains () {
 	local seeking="${2}"
 	local in=1
 	for element in "${!array-}"; do
-		if [[ "$element" == "$seeking" ]]; then
+		if [[ "${element}" == "${seeking}" ]]; then
 			in=0
 			break
 		fi
@@ -44,8 +44,6 @@ module load "${htsLibVersion}"
 #Check modules
 module list
 
-echo "## $(date) Start $0"
-
 INPUTS=()
 ALLGVCFs=()
 
@@ -55,21 +53,21 @@ do
 done
 
 SAMPLESIZE=${#INPUTS[@]}
-numberofbatches=$(($SAMPLESIZE / 200))
+numberofbatches=$(("${SAMPLESIZE}" / 200))
 
-for b in $(seq 0 $numberofbatches)
+for b in $(seq 0 "${numberofbatches}")
 do
-	if [ -f ${gatkHaplotypeCallerGvcf}.$b ]
+	if [[ -f "${gatkHaplotypeCallerGvcf}.${b}" ]]
 	then
-		ALLGVCFs+=("--variant gatkHaplotypeCallerGvcf}.$b")
+		ALLGVCFs+=("--variant ${gatkHaplotypeCallerGvcf}.${b}")
 	fi
 done
 
-if [ "${SAMPLESIZE}" -gt 200 ]
+if [[ "${SAMPLESIZE}" -gt 200 ]]
 then
 	for b in $(seq 0 "${numberofbatches}")
 	do
-		if [ -f "${projectBatchCombinedVariantCalls}.${b}" ]
+		if [[ -f "${projectBatchCombinedVariantCalls}.${b}" ]]
 		then
 			ALLGVCFs+=("--variant=${projectBatchCombinedVariantCalls}.${b}")
 		fi
@@ -77,9 +75,9 @@ then
 else
 	for sampleGvcf in "${gatkHaplotypeCallerGvcf[@]}"
 	do
-		if [ -f "${sampleGvcf}" ]
+		if [[ -f "${sampleGvcf}" ]]
 		then
-			array_contains ALLGVCFs "--variant=${sampleGvcf}" || ALLGVCFs+=("--variant=$sampleGvcf")
+			array_contains ALLGVCFs "--variant=${sampleGvcf}" || ALLGVCFs+=("--variant=${sampleGvcf}")
 		fi
 	done
 fi
@@ -87,7 +85,7 @@ fi
 
 GvcfSize=${#ALLGVCFs[@]}
 
-if [ ${GvcfSize} -ne 0 ]
+if [[ ${GvcfSize} -ne 0 ]]
 then
 
 	gatk --java-options "-Xmx5g -Djava.io.tmpdir=${tmpTmpDataDir}" CombineGVCFs \
@@ -106,11 +104,11 @@ then
 
 	tabix -p vcf "${projectBatchGenotypedVariantCalls}"
 
-	printf "${projectBatchGenotypedVariantCalls} ..done\n"
+	echo "${projectBatchGenotypedVariantCalls} ..done"
 
-	cd "${intermediateDir}"
-	md5sum $(basename "${projectBatchGenotypedVariantCalls}")> $(basename "${projectBatchGenotypedVariantCalls}").md5
-	cd -
+	cd "${intermediateDir}" || exit
+	md5sum "$(basename "${projectBatchGenotypedVariantCalls}")" > "$(basename "${projectBatchGenotypedVariantCalls}").md5"
+	cd - || exit 
 	echo "succes moving files"
 
 else
diff --git a/protocols/GatkHaplotypeCallerGvcf.sh b/protocols/GatkHaplotypeCallerGvcf.sh
index 678b07d..2349314 100755
--- a/protocols/GatkHaplotypeCallerGvcf.sh
+++ b/protocols/GatkHaplotypeCallerGvcf.sh
@@ -23,13 +23,11 @@ makeTmpDir "${gatkHaplotypeCallerGvcftbi}"
 tmpGatkHaplotypeCallerGvcftbi=${MC_tmpFile}
 
 #Load modules
-module load ${gatkVersion}
+module load "${gatkVersion}"
 
 #Check modules
 module list
 
-echo "## "$(date)" Start $0"
-
 gatk --java-options "-XX:ParallelGCThreads=1 -Djava.io.tmpdir=${tmpTmpDataDir} -Xmx12g" HaplotypeCaller \
 -R "${indexFile}" \
 -I "${bqsrBam}" \
@@ -39,8 +37,3 @@ gatk --java-options "-XX:ParallelGCThreads=1 -Djava.io.tmpdir=${tmpTmpDataDir} -
 
 mv "${tmpGatkHaplotypeCallerGvcf}" "${gatkHaplotypeCallerGvcf}"
 mv "${tmpGatkHaplotypeCallerGvcftbi}" "${gatkHaplotypeCallerGvcftbi}"
-
-echo "returncode: $?";
-echo "succes moving files";
-
-echo "## "$(date)" ##  $0 Done "
diff --git a/protocols/HTSeq_count.sh b/protocols/HTSeq_count.sh
index 62d2bdf..cd6c0b6 100755
--- a/protocols/HTSeq_count.sh
+++ b/protocols/HTSeq_count.sh
@@ -34,7 +34,7 @@ then
 	if [[ "${num1}" > 0.6 ]]
 	then
 		STRANDED="yes"
-	elif [[ "${num2}" > 0.6  ]]
+	elif [[ "${num2}" > 0.6 ]]
 	then
 		STRANDED="reverse"
 	elif [[ "${num1}" < 0.6 && "${num2}" < 0.6 ]]
diff --git a/protocols/IndelRealignment.sh b/protocols/IndelRealignment.sh
index 915a90f..246fa3a 100755
--- a/protocols/IndelRealignment.sh
+++ b/protocols/IndelRealignment.sh
@@ -33,14 +33,9 @@ module load "${gatkVersion}"
 #check modules
 module list
 
-echo "## $(date) Start $0"
-
-echo
-echo
 echo "Running GATK IndelRealignment:"
 
-
-java -Xmx10g -XX:ParallelGCThreads=8 -Djava.io.tmpdir="${tmpTmpDataDir}" -jar "$EBROOTGATK/GenomeAnalysisTK.jar" \
+java -Xmx10g -XX:ParallelGCThreads=8 -Djava.io.tmpdir="${tmpTmpDataDir}" -jar "${EBROOTGATK}/GenomeAnalysisTK.jar" \
 -T IndelRealigner \
 -R "${indexFile}" \
 -I "${splitAndTrimBam}" \
@@ -55,7 +50,5 @@ java -Xmx10g -XX:ParallelGCThreads=8 -Djava.io.tmpdir="${tmpTmpDataDir}" -jar "$
 mv "${tmpIndelRealignedBam}" "${IndelRealignedBam}"
 mv "${tmpIndelRealignedBai}" "${IndelRealignedBai}"
 
-echo "returncode: $?";
 echo "succes moving files";
-echo "## $(date) ##  $0 Done "
 
diff --git a/protocols/Leafcutter_intron_clustering.sh b/protocols/Leafcutter_intron_clustering.sh
index dd21168..bafb37c 100755
--- a/protocols/Leafcutter_intron_clustering.sh
+++ b/protocols/Leafcutter_intron_clustering.sh
@@ -27,7 +27,7 @@ echo -e "\nWith strandedness type: ${STRANDED},
 where (0 = unstranded, 1 = first-strand/RF, 2, = second-strand/FR)."
 
 rm -f "${intermediateDir}${project}_juncfiles.txt"
-cd "${intermediateDir}"
+cd "${intermediateDir}" || exit
 for bamfile in *."${sampleMergedBamExt}"
 do
 
@@ -54,4 +54,4 @@ python "${EBROOTLEAFCUTTER}/clustering/leafcutter_cluster_regtools.py" \
 -l 500000 \
 --nochromcheck=NOCHROMCHECK
 
-cd -
+cd - || exit
diff --git a/protocols/MakeExpressionTable.sh b/protocols/MakeExpressionTable.sh
index 7eb5477..10aeb40 100755
--- a/protocols/MakeExpressionTable.sh
+++ b/protocols/MakeExpressionTable.sh
@@ -18,7 +18,7 @@ array_contains () {
 	local seeking="${2}"
 	local in=1
 	for element in "${!array-}"; do
-		if [[ "$element" == "$seeking" ]]; then
+		if [[ "${element}" == "${seeking}" ]]; then
 			in=0
 			break
 		fi
@@ -45,7 +45,7 @@ done
 python "${EBROOTNGS_RNA}/scripts/create_counts_matrix.py" \
 -i "${intermediateDir}/fileList.txt" \
 -o "${tmpProjectHTseqExpressionTable}" \
--e "$intermediateDir/create_counts_matrix.log"
+-e "${intermediateDir}/create_counts_matrix.log"
 
 echo "table create succesfull"
 mv "${tmpProjectHTseqExpressionTable}" "${projectHTseqExpressionTable}"
diff --git a/protocols/MarkDuplicates.sh b/protocols/MarkDuplicates.sh
index b86d02b..8ae64c1 100755
--- a/protocols/MarkDuplicates.sh
+++ b/protocols/MarkDuplicates.sh
@@ -57,7 +57,7 @@ sambamba markdup \
 mv "${tmpSampleMergedDedupBam}" "${sampleMergedDedupBam}"
 mv "${tmpSampleMergedDedupBai}" "${sampleMergedDedupBai}"
 
-cd "${intermediateDir}"
-md5sum "${sampleMergedDedupBam}" > $(basename "${sampleMergedDedupBam}").md5
-md5sum "${sampleMergedDedupBai}" > $(basename "${sampleMergedDedupBai}").md5
-cd -
+cd "${intermediateDir}" || exit
+md5sum "${sampleMergedDedupBam}" > "$(basename "${sampleMergedDedupBam}").md5"
+md5sum "${sampleMergedDedupBai}" > "$(basename "${sampleMergedDedupBai}").md5"
+cd - || exit
diff --git a/protocols/MergeBam.sh b/protocols/MergeBam.sh
index aa5ced4..6c633e3 100755
--- a/protocols/MergeBam.sh
+++ b/protocols/MergeBam.sh
@@ -58,14 +58,14 @@ done
 
 if [[ "${#INPUTS[@]}" == 1 ]]
 then
-	ln -sf $(basename "${INPUTBAMS[0]}") "${sampleMergedBam}"
-	ln -sf $(basename "${UNIQUEBAIS[0]}") "${sampleMergedBai}"
+	ln -sf "$(basename "${INPUTBAMS[0]}")" "${sampleMergedBam}"
+	ln -sf "$(basename "${UNIQUEBAIS[0]}")" "${sampleMergedBai}"
 	echo "nothing to merge because there is only one sample"
 
-	cd "${intermediateDir}"
-	md5sum $(basename "${sampleMergedBam}")> $(basename "${sampleMergedBam}").md5sum
-	md5sum $(basename "${sampleMergedBai}")> $(basename "${sampleMergedBai}").md5sum
-	cd -
+	cd "${intermediateDir}" || exit
+	md5sum "$(basename "${sampleMergedBam}")" > "$(basename "${sampleMergedBam}").md5sum"
+	md5sum "$(basename "${sampleMergedBai}")" > "$(basename "${sampleMergedBai}").md5sum"
+	cd - || exit
 
 else
 	java -XX:ParallelGCThreads=4 -jar -Xmx6g "${EBROOTPICARD}/${picardJar}" "${mergeSamFilesJar}" \
@@ -82,8 +82,8 @@ else
 	mv "${tmpSampleMergedBam}" "${sampleMergedBam}"
 	mv "${tmpSampleMergedBai}" "${sampleMergedBai}"
 
-	cd "${intermediateDir}"
-	md5sum $(basename "${sampleMergedBam}")> $(basename "${sampleMergedBam}").md5sum
-	md5sum $(basename "${sampleMergedBai}")> $(basename "${sampleMergedBai}").md5sum
-	cd -
+	cd "${intermediateDir}" || exit
+	md5sum "$(basename "${sampleMergedBam}")" > "$(basename "${sampleMergedBam}").md5sum"
+	md5sum "$(basename "${sampleMergedBai}")" > "$(basename "${sampleMergedBai}").md5sum"
+	cd - || exit
 fi
diff --git a/protocols/MultiQCReport.sh b/protocols/MultiQCReport.sh
index 37fdd48..557a0f8 100755
--- a/protocols/MultiQCReport.sh
+++ b/protocols/MultiQCReport.sh
@@ -94,4 +94,4 @@ multiqc -c "/intermediateDir/${project}_QC_config.yaml" \
 -f "/intermediateDir/" \
 -o "/projectResultsDir/"
 
-mv ${projectResultsDir}/multiqc_report.html ${projectResultsDir}/${project}_multiqc_report.html
+mv "${projectResultsDir}/multiqc_report.html" "${projectResultsDir}/${project}_multiqc_report.html"
diff --git a/protocols/OUTRIDER.sh b/protocols/OUTRIDER.sh
index 7bd6fc5..d50cc5c 100755
--- a/protocols/OUTRIDER.sh
+++ b/protocols/OUTRIDER.sh
@@ -25,7 +25,7 @@ do
 	mkdir -p "${projectResultsDir}/outrider/${sample}/QC"
 done
 #run outrider QC part
-singularity exec --pwd $PWD --bind "${sifDir}:/sifDir,/apps:/apps,/groups:/groups" \
+singularity exec --pwd "${PWD}" --bind "${sifDir}:/sifDir,/apps:/apps,/groups:/groups" \
 "${sifDir}/${outriderVersion}" \
 Rscript "${EBROOTNGS_RNA}/scripts/outrider-qc.R" \
 "${projectHTseqExpressionTable}" \
@@ -45,7 +45,7 @@ do
 		#get geneOfInterest from samplessheet of provided,
 		#or else get top 3 most significate genes from outrider output.
 		GENE="${geneOfInterest[samplenumber]}"
-		if [[ ! -z "${GENE}" ]]
+		if [[ -n "${GENE}" ]]
 		then
 			echo "${GENE}" > "${projectResultsDir}/outrider/${sample}/${sample}.genesOfInterest.tsv"
 		else
@@ -55,7 +55,7 @@ do
 done
 
 #Run outrider to genarate plots per sample, and top 3 significant gene.
-singularity exec --pwd $PWD --bind "${sifDir}:/sifDir,/apps:/apps,/groups:/groups" \
+singularity exec --pwd "${PWD}" --bind "${sifDir}:/sifDir,/apps:/apps,/groups:/groups" \
 "${sifDir}/${outriderVersion}" \
 Rscript "${EBROOTNGS_RNA}/scripts/outrider.R" \
 "${projectResultsDir}/outrider/"
diff --git a/protocols/QCStats.sh b/protocols/QCStats.sh
index 2360b76..eb87b19 100755
--- a/protocols/QCStats.sh
+++ b/protocols/QCStats.sh
@@ -40,9 +40,6 @@ module load "${pythonVersion}"
 module load "${ngsVersion}"
 module list
 
-makeTmpDir "${intermediateDir}"
-tmpIntermediateDir="${MC_tmpFile}"
-
 # Get strandness.
 STRANDED="$(num1="$(tail -n 2 "${strandedness}" | awk '{print $7}' | head -n 1)"; num2="$(tail -n 2 "${strandedness}" | awk '{print $7}' | tail -n 1)"; if (( $(echo "$num1 > 0.6" | bc -l) )); then echo "SECOND_READ_TRANSCRIPTION_STRAND"; fi; if (( $(echo "$num2 > 0.6" | bc -l) )); then echo "FIRST_READ_TRANSCRIPTION_STRAND"; fi; if (( $(echo "$num1 < 0.6 && $num2 < 0.6" | bc -l) )); then echo "NONE"; fi)"
 
@@ -52,15 +49,15 @@ then
 	echo -e "generate CollectMultipleMetrics"
 
 	# Picard CollectMultipleMetrics
-		java -jar -Xmx6g -XX:ParallelGCThreads=4 "${EBROOTPICARD}/${picardJar}" CollectMultipleMetrics \
-		I="${sampleMergedDedupBam}" \
-		O="${collectMultipleMetricsPrefix}" \
-		R="${indexSpecies}" \
-		PROGRAM=CollectAlignmentSummaryMetrics \
-		PROGRAM=QualityScoreDistribution \
-		PROGRAM=MeanQualityByCycle \
-		PROGRAM=CollectInsertSizeMetrics \
-		TMP_DIR="${tempDir}/processing"
+	java -jar -Xmx6g -XX:ParallelGCThreads=4 "${EBROOTPICARD}/${picardJar}" CollectMultipleMetrics \
+	I="${sampleMergedDedupBam}" \
+	O="${collectMultipleMetricsPrefix}" \
+	R="${indexSpecies}" \
+	PROGRAM=CollectAlignmentSummaryMetrics \
+	PROGRAM=QualityScoreDistribution \
+	PROGRAM=MeanQualityByCycle \
+	PROGRAM=CollectInsertSizeMetrics \
+	TMP_DIR="${tempDir}/processing"
 
 
 	#Flagstat for reads mapping to the genome.
@@ -85,32 +82,32 @@ then
 elif [[ "${seqType}" == "SR" ]]
 then
 
-		#Flagstat for reads mapping to the genome.
-		samtools flagstat "${sampleMergedDedupBam}" > "${flagstatMetrics}"
+	#Flagstat for reads mapping to the genome.
+	samtools flagstat "${sampleMergedDedupBam}" > "${flagstatMetrics}"
 
 	# Fagstats idxstats, reads per chr.
-		samtools idxstats "${sampleMergedDedupBam}" > "${idxstatsMetrics}"
+	samtools idxstats "${sampleMergedDedupBam}" > "${idxstatsMetrics}"
 
 	echo -e "generate CollectMultipleMetrics"
 
-		# Picard CollectMultipleMetrics
-		java -jar -Xmx6g -XX:ParallelGCThreads=4 "${EBROOTPICARD}/${picardJar}" CollectMultipleMetrics \
-		I="${sampleMergedDedupBam}" \
-		O="${collectMultipleMetricsPrefix}" \
-		R="${indexSpecies}" \
-		PROGRAM=CollectAlignmentSummaryMetrics \
-		PROGRAM=QualityScoreDistribution \
-		PROGRAM=MeanQualityByCycle \
-		PROGRAM=CollectInsertSizeMetrics \
-		TMP_DIR="${tempDir}/processing"
-
-		#CollectRnaSeqMetrics.jar
-		java -XX:ParallelGCThreads=4 -jar -Xmx6g "${EBROOTPICARD}/${picardJar}" CollectRnaSeqMetrics \
-		REF_FLAT="${annotationRefFlat}" \
-		I="${sampleMergedDedupBam}" \
-		STRAND_SPECIFICITY="${STRANDED}" \
-		RIBOSOMAL_INTERVALS="${annotationIntervalList}" \
-		VALIDATION_STRINGENCY=LENIENT \
-		O="${rnaSeqMetrics}" \
-		CHART_OUTPUT="${rnaSeqMetrics}.pdf"
+	# Picard CollectMultipleMetrics
+	java -jar -Xmx6g -XX:ParallelGCThreads=4 "${EBROOTPICARD}/${picardJar}" CollectMultipleMetrics \
+	I="${sampleMergedDedupBam}" \
+	O="${collectMultipleMetricsPrefix}" \
+	R="${indexSpecies}" \
+	PROGRAM=CollectAlignmentSummaryMetrics \
+	PROGRAM=QualityScoreDistribution \
+	PROGRAM=MeanQualityByCycle \
+	PROGRAM=CollectInsertSizeMetrics \
+	TMP_DIR="${tempDir}/processing"
+
+	#CollectRnaSeqMetrics.jar
+	java -XX:ParallelGCThreads=4 -jar -Xmx6g "${EBROOTPICARD}/${picardJar}" CollectRnaSeqMetrics \
+	REF_FLAT="${annotationRefFlat}" \
+	I="${sampleMergedDedupBam}" \
+	STRAND_SPECIFICITY="${STRANDED}" \
+	RIBOSOMAL_INTERVALS="${annotationIntervalList}" \
+	VALIDATION_STRINGENCY=LENIENT \
+	O="${rnaSeqMetrics}" \
+	CHART_OUTPUT="${rnaSeqMetrics}.pdf"
 fi
diff --git a/protocols/STAR.sh b/protocols/STAR.sh
index b837927..16f7a2b 100755
--- a/protocols/STAR.sh
+++ b/protocols/STAR.sh
@@ -25,15 +25,12 @@ module list
 makeTmpDir "${intermediateDir}"
 tmpintermediateDir=${MC_tmpFile}
 
-echo "## $(date) Start $0"
-echo "ID (internalSampleID-lane): ${externalSampleID}"
-
 if [[ "${seqType}" == 'SR' ]]
 then
-	echo "seqType = "${seqType}";FastQ: ${mergedSingleBarcodeFqGz}"
+	echo "seqType = ${seqType}; FastQ: ${mergedSingleBarcodeFqGz}"
 	inputs="--readFilesIn ${mergedSingleBarcodeFqGz}"
 else
-	echo "seqType = "${seqType}";FastQs: ${mergedLeftBarcodeFqGz} ${mergedRightBarcodeFqGz}"
+	echo "seqType = ${seqType}; FastQs: ${mergedLeftBarcodeFqGz} ${mergedRightBarcodeFqGz}"
 	inputs="--readFilesIn ${mergedLeftBarcodeFqGz} ${mergedRightBarcodeFqGz}"
 fi
 
@@ -62,4 +59,3 @@ echo "STAR for RNA"
 	mv -f "${tmpintermediateDir}/${externalSampleID}."* "${intermediateDir}"
 
 echo "succes moving files";
-echo "## $(date) ##  $0 Done "
diff --git a/protocols/SplitAndTrim.sh b/protocols/SplitAndTrim.sh
index c6aa646..93ee94a 100755
--- a/protocols/SplitAndTrim.sh
+++ b/protocols/SplitAndTrim.sh
@@ -35,10 +35,6 @@ module load "${samtoolsVersion}"
 #check modules
 module list
 
-echo "## $(date) Start $0"
-
-echo "Running split and trim:"
-
 java -Xmx10g -XX:ParallelGCThreads=2 \
 -Djava.io.tmpdir="${tmpTmpDataDir}" \
 -jar "${EBROOTGATK}/gatk-package-4.1.4.1-local.jar" SplitNCigarReads \
@@ -52,12 +48,8 @@ mv "${tmpsplitAndTrimBai}" "${splitAndTrimBai}"
 
 # Create md5sum for zip file
 
-cd "${intermediateDir}"
+cd "${intermediateDir}" || exit
 md5sum "${splitAndTrimShortBam}" > "${splitAndTrimShortBam}.md5"
 md5sum "${splitAndTrimShortBai}" > "${splitAndTrimShortBai}.md5"
-echo "returncode: $?";
-echo "succes moving files";
-cd -
-
-echo "## $(date) ##  $0 Done "
+cd - || exit
 
diff --git a/protocols/Stranded.sh b/protocols/Stranded.sh
index b5d37a6..a285527 100755
--- a/protocols/Stranded.sh
+++ b/protocols/Stranded.sh
@@ -17,15 +17,8 @@ makeTmpDir "${strandedness}"
 tmpStrandedness=${MC_tmpFile}
 
 
-echo "## $(date) Start $0"
-
-i=$(ls "${intermediateDir}"/*.Aligned.sortedByCoord.out.bam -1 |shuf -n 1)
+i=$(find "${intermediateDir}" -name "*.Aligned.sortedByCoord.out.bam" | shuf -n 1)
 
 infer_experiment.py -r "${bed12}" -i "${i}" > "${tmpStrandedness}"
 
 mv "${tmpStrandedness}" "${strandedness}"
-
-echo "succes moving files";
-echo "## $(date) ##  $0 Done "
-
-
diff --git a/protocols/TIN.sh b/protocols/TIN.sh
index eada468..b796d8d 100755
--- a/protocols/TIN.sh
+++ b/protocols/TIN.sh
@@ -16,13 +16,11 @@
 #string tmpName
 #string logsDir
 
-echo "## $(date) Start $0"
-
 makeTmpDir "${intermediateDir}"
 tmpintermediateDir=${MC_tmpFile}
 
 mkdir -p "${tinDir}"
-cd "${tinDir}"
+cd "${tinDir}" || exit
 
 # Extract the alignment of housekeeping genes.
 module load "${bedToolsVersion}"
@@ -44,7 +42,5 @@ tin.py \
 
 mv "${tmpintermediateDir}/${externalSampleID}"* "${intermediateDir}"
 
-cd -
+cd - || exit
 
-echo "succes moving files";
-echo "## $(date) ##  $0 Done "
diff --git a/protocols/GatkMergeGvcf.sh b/protocols/deprecated/GatkMergeGvcf.sh
similarity index 87%
rename from protocols/GatkMergeGvcf.sh
rename to protocols/deprecated/GatkMergeGvcf.sh
index 1623bc3..fa8fc2b 100755
--- a/protocols/GatkMergeGvcf.sh
+++ b/protocols/deprecated/GatkMergeGvcf.sh
@@ -29,7 +29,7 @@ array_contains () {
 	local seeking="${2}"
 	local in=1
 	for element in "${!array-}"; do
-		if [[ "$element" == "$seeking" ]]; then
+		if [[ "${element}" == "${seeking}" ]]; then
 			in=0
 			break
 		fi
@@ -38,19 +38,17 @@ array_contains () {
 }
 
 #Load modules
-module load ${gatkVersion}
+module load "${gatkVersion}"
 
 #Check modules
 module list
 
-echo "## $(date) Start $0"
-
 INPUTS=()
 ALLGVCFs=()
 
 for external in "${externalSampleID[@]}"
 do
-	array_contains INPUTS "${external}" || INPUTS+=("$external")    # If vcfFile does not exist in array add it
+	array_contains INPUTS "${external}" || INPUTS+=("${external}")    # If vcfFile does not exist in array add it
 done
 
 SAMPLESIZE="${#INPUTS[@]}"
@@ -95,8 +93,8 @@ if [[ "${gvcfSize}" -ne 0 ]]
 then
 	for i in "${tmpProjectBatchCombinedVariantCalls}".*
 	do
-		mv "${i}" "${intermediateDir}"/$(basename "${i}")
-		echo "mv $i ${intermediateDir}/$(basename $i)"
+		mv "${i}" "${intermediateDir}/$(basename "${i}")"
+		echo "mv ${i} ${intermediateDir}/$(basename "${i}")"
 	done
 else
 	echo "nothing to move! There are no samples, maybe there is something going wrong, or maybe chrX or chrY are not in the bed file"
diff --git a/protocols/filter_Leafcutter.sh b/protocols/deprecated/filter_Leafcutter.sh
similarity index 93%
rename from protocols/filter_Leafcutter.sh
rename to protocols/deprecated/filter_Leafcutter.sh
index f03ab60..2345d1d 100755
--- a/protocols/filter_Leafcutter.sh
+++ b/protocols/deprecated/filter_Leafcutter.sh
@@ -1,3 +1,4 @@
+
 #MOLGENIS nodes=1 ppn=1 mem=34gb walltime=05:00:00
 
 #Parameter mapping
@@ -18,8 +19,6 @@ module load "${python2Version}"
 module list
 
 
-
-INPUTFILE="${intermediateDir}${externalSampleID}.leafcutter.outlier_cluster_significance.txt"
 OUTPUTFILE="${intermediateDir}${externalSampleID}.leafcutter.report.tsv"
 
 # adding coordinates to leafcutter results
diff --git a/protocols/rMATs.sh b/protocols/rMATs.sh
index a287fbc..992cff6 100755
--- a/protocols/rMATs.sh
+++ b/protocols/rMATs.sh
@@ -29,7 +29,7 @@ rm -r "${rMATsOutputDir}/${externalSampleID}/tmp/"
 while read -r line
 do
 	# reading each line
-	read name status <<< "${line}"
+	read -r name status <<< "${line}"
 	if [[ "${status}" == "sample" ]]
 	then
 		echo "${name} is a ${status} : in ${externalSampleID}.B1.txt"

From cc5b95e23d3533a231b7b1e0a0975a00556d009f Mon Sep 17 00:00:00 2001
From: gerbenvandervries <gerbenvandervries@gmail.com>
Date: Thu, 12 Jan 2023 10:25:55 +0100
Subject: [PATCH 12/42] added pipefail, fixes for shellcheck

---
 check/shellcheck.sh                       | 13 ++--
 protocols/AddOrReplaceReadGroups.sh       |  2 +-
 protocols/BQSR.sh                         |  1 +
 protocols/CombineFastq.sh                 |  1 +
 protocols/CopyPrmTmpData.sh               |  1 +
 protocols/CopyToResultsDir.sh             |  1 +
 protocols/CreateExternSamplesProjects.sh  |  1 +
 protocols/CreateInhouseRnaSeqProjects.sh  |  1 +
 protocols/DE.sh                           |  2 +
 protocols/Design.sh                       |  1 +
 protocols/FastQC.sh                       |  1 +
 protocols/GatkGenotypeGvcf.sh             |  1 +
 protocols/GatkHaplotypeCallerGvcf.sh      |  1 +
 protocols/HTSeq_count.sh                  | 24 ++----
 protocols/IndelRealignment.sh             |  1 +
 protocols/Leafcutter.sh                   | 14 +++-
 protocols/Leafcutter_filter.sh            |  1 +
 protocols/Leafcutter_intron_clustering.sh |  9 +--
 protocols/Leafcutter_rare.sh              |  1 +
 protocols/MakeExpressionTable.sh          |  1 +
 protocols/MarkDuplicates.sh               |  1 +
 protocols/MergeBam.sh                     |  1 +
 protocols/MultiQCReport.sh                | 94 +++++++++++------------
 protocols/OUTRIDER.sh                     |  1 +
 protocols/QCStats.sh                      |  6 +-
 protocols/RNASeQC.sh                      |  1 +
 protocols/RNASeQCPlots.sh                 |  1 +
 protocols/STAR.sh                         |  1 +
 protocols/SplitAndTrim.sh                 |  1 +
 protocols/Stranded.sh                     |  1 +
 protocols/TIN.sh                          |  1 +
 protocols/TrimReads_TrimGalore.sh         |  1 +
 protocols/VIP.sh                          | 17 ++--
 protocols/annotate_SJ_with_SJDB.sh        |  1 +
 protocols/create_SJDB.sh                  |  1 +
 protocols/normalize_SJ.sh                 |  1 +
 protocols/rMATs.sh                        |  8 +-
 protocols/rMats_reformat.sh               |  1 +
 38 files changed, 127 insertions(+), 90 deletions(-)

diff --git a/check/shellcheck.sh b/check/shellcheck.sh
index 6f2d5a8..23bc1d9 100755
--- a/check/shellcheck.sh
+++ b/check/shellcheck.sh
@@ -7,10 +7,12 @@
 #  * SC2015: Note that A && B || C is not if-then-else. C may run when A is true.
 #            We know and use this construct regularly to create "transactions"
 #            where C is only executed when both A and B have succeeded.
-#  * SC2148  Tips depend on target shell and yours is unknown. Add a shebang or a 'shell' directive. Not needed for Molgenis Compute protocols.
-#  * SC2154  Not deeded, Molgenis Compute takes care of this.
+#  * SC2154: Due to Molgenis Compute string initialization the warning is not valid 
 #
-export SHELLCHECK_OPTS="-e SC2004 -e SC2015 -e SC2148 -e SC2154"
+#  * SC2148: the shebang is declared in the header.ftl not in the protocols
+#
+
+export SHELLCHECK_OPTS="-e SC2004 -e SC2015 -e SC2154 -e SC2148"
 
 function showHelp() {
 	#
@@ -33,7 +35,7 @@ EOH
 #
 # Parse commandline options
 #
-while getopts "hv" opt
+while getopts ":hv" opt
 do
 	case "${opt}" in
 		h)
@@ -89,7 +91,8 @@ then
 	#	https://github.com/koalaman/shellcheck/wiki/SC${ISSUENUMBER}
 	# explaining what is wrong with the code / style and how to improve it.
 	#
-	perl -pi -e "s|message='([^']+)'\s+source='ShellCheck.(SC[0-9]+)'|message='&lt;a href=&quot;https://github.com/koalaman/shellcheck/wiki/\$2&quot;&gt;\$2: \$1&lt;/a&gt;' source='ShellCheck.\$2'|" checkstyle-result.xml
+	perl -pi -e "s|message='([^']+)'\s+source='ShellCheck.(SC[0-9]+)'|message='&lt;a href=&quot;https://github.com/koalaman/shellcheck/wiki/\$2&quot;&gt;\$2: 
+\$1&lt;/a&gt;' source='ShellCheck.\$2'|" checkstyle-result.xml
 else
 	#
 	# ShellCheck for regular user on the commandline.
diff --git a/protocols/AddOrReplaceReadGroups.sh b/protocols/AddOrReplaceReadGroups.sh
index 5fac966..d41868e 100755
--- a/protocols/AddOrReplaceReadGroups.sh
+++ b/protocols/AddOrReplaceReadGroups.sh
@@ -1,4 +1,4 @@
-#!/bin/bash
+set -o pipefail
 #MOLGENIS nodes=1 ppn=8 mem=8gb walltime=05:00:00
 
 #string project
diff --git a/protocols/BQSR.sh b/protocols/BQSR.sh
index 825aa1d..eba2f22 100755
--- a/protocols/BQSR.sh
+++ b/protocols/BQSR.sh
@@ -1,3 +1,4 @@
+set -o pipefail
 #MOLGENIS nodes=1 ppn=8 mem=15gb walltime=23:59:00
 
 #string project
diff --git a/protocols/CombineFastq.sh b/protocols/CombineFastq.sh
index 7817a2c..9fc3596 100644
--- a/protocols/CombineFastq.sh
+++ b/protocols/CombineFastq.sh
@@ -1,3 +1,4 @@
+set -o pipefail
 #MOLGENIS walltime=23:59:00 mem=8gb ppn=6
 
 #Parameter mapping
diff --git a/protocols/CopyPrmTmpData.sh b/protocols/CopyPrmTmpData.sh
index 761a4bf..d3a4c0a 100755
--- a/protocols/CopyPrmTmpData.sh
+++ b/protocols/CopyPrmTmpData.sh
@@ -1,3 +1,4 @@
+set -o pipefail
 #MOLGENIS walltime=01:59:00 mem=4gb
 
 #string allRawNgstmpDataDir
diff --git a/protocols/CopyToResultsDir.sh b/protocols/CopyToResultsDir.sh
index 7fa671e..8ee5487 100755
--- a/protocols/CopyToResultsDir.sh
+++ b/protocols/CopyToResultsDir.sh
@@ -1,3 +1,4 @@
+set -o pipefail
 #MOLGENIS walltime=23:59:00 nodes=1 cores=1 mem=4gb
 
 #Parameter mapping
diff --git a/protocols/CreateExternSamplesProjects.sh b/protocols/CreateExternSamplesProjects.sh
index c22799c..c4644da 100755
--- a/protocols/CreateExternSamplesProjects.sh
+++ b/protocols/CreateExternSamplesProjects.sh
@@ -1,3 +1,4 @@
+set -o pipefail
 #MOLGENIS walltime=02:00:00 mem=4gb
 
 #list seqType
diff --git a/protocols/CreateInhouseRnaSeqProjects.sh b/protocols/CreateInhouseRnaSeqProjects.sh
index 88dc334..e3ee4c7 100755
--- a/protocols/CreateInhouseRnaSeqProjects.sh
+++ b/protocols/CreateInhouseRnaSeqProjects.sh
@@ -1,3 +1,4 @@
+set -o pipefail
 #MOLGENIS walltime=10-23:59:00 mem=2gb ppn=2
 
 #list seqType
diff --git a/protocols/DE.sh b/protocols/DE.sh
index f0e0923..b30ac6a 100755
--- a/protocols/DE.sh
+++ b/protocols/DE.sh
@@ -1,3 +1,4 @@
+set -o pipefail
 #MOLGENIS nodes=1 ppn=4 mem=4gb walltime=05:59:00
 
 #Parameter mapping
@@ -41,6 +42,7 @@ cd "${intermediateDir}" || exit
 
 #detect number of conditions
 col=$(col="condition"; head -n1 "${projectJobsDir}/${project}.csv" | tr "," "\n" | grep -n "${col}")
+# shellcheck disable=SC2206
 colArray=(${col//:/ })
 conditionCount=$(tail -n +2 "${projectJobsDir}/${project}.csv" | cut -d "," -f "${colArray[0]}" | sort | uniq | wc -l)
 
diff --git a/protocols/Design.sh b/protocols/Design.sh
index ba33b14..041e16f 100755
--- a/protocols/Design.sh
+++ b/protocols/Design.sh
@@ -1,3 +1,4 @@
+set -o pipefail
 #MOLGENIS nodes=1 ppn=4 mem=4gb walltime=05:59:00
 
 #Parameter mapping
diff --git a/protocols/FastQC.sh b/protocols/FastQC.sh
index 509589f..5b519d8 100755
--- a/protocols/FastQC.sh
+++ b/protocols/FastQC.sh
@@ -1,3 +1,4 @@
+set -o pipefail
 #MOLGENIS nodes=1 ppn=1 mem=1gb walltime=05:00:00
 
 
diff --git a/protocols/GatkGenotypeGvcf.sh b/protocols/GatkGenotypeGvcf.sh
index 19ad9f7..1fc52f4 100755
--- a/protocols/GatkGenotypeGvcf.sh
+++ b/protocols/GatkGenotypeGvcf.sh
@@ -1,3 +1,4 @@
+set -o pipefail
 #MOLGENIS walltime=23:59:00 mem=17gb ppn=3 nodes=1
 
 #string gatkVersion
diff --git a/protocols/GatkHaplotypeCallerGvcf.sh b/protocols/GatkHaplotypeCallerGvcf.sh
index 2349314..e7b724e 100755
--- a/protocols/GatkHaplotypeCallerGvcf.sh
+++ b/protocols/GatkHaplotypeCallerGvcf.sh
@@ -1,3 +1,4 @@
+set -o pipefail
 #MOLGENIS walltime=23:59:00 mem=12gb ppn=8 nodes=1
 
 #string gatkVersion
diff --git a/protocols/HTSeq_count.sh b/protocols/HTSeq_count.sh
index cd6c0b6..b25ccc9 100755
--- a/protocols/HTSeq_count.sh
+++ b/protocols/HTSeq_count.sh
@@ -1,3 +1,4 @@
+set -o pipefail
 #MOLGENIS walltime=24:00:00 nodes=1 cores=1 mem=6gb
 
 #Parameter mapping
@@ -29,23 +30,14 @@ ROWNR=$(wc -l "${strandedness}" | awk '{ print $1 }')
 
 if [[ "${ROWNR}" == 6 ]]
 then
-	num1=$(tail -n 2 "${strandedness}" | awk '{print $7}' | head -n 1)
-	num2=$(tail -n 2 "${strandedness}" | awk '{print $7}' | tail -n 1)
-	if [[ "${num1}" > 0.6 ]]
-	then
-		STRANDED="yes"
-	elif [[ "${num2}" > 0.6 ]]
-	then
-		STRANDED="reverse"
-	elif [[ "${num1}" < 0.6 && "${num2}" < 0.6 ]]
-	then
-		STRANDED="no"
-	else
-		STRANDED="no"
-	fi
+	num1="$(tail -n 2 "${strandedness}" | awk '{print $7}' | head -n 1)"
+	num2="$(tail -n 1 "${strandedness}" | awk '{print $7}')"
+
+	STRANDED=$(echo -e "${num1}\t${num2}" | awk '{if ($1 > 0.6){print "yes"}else if($2 > 0.6){print "reverse"}else if($1 < 0.6 && $2 < 0.6){print "no"} }')
+
 else
-	echo "strandedness detection failed"
-	STRANDED='no'
+	echo "strandedness detection failed, STRANDED='yes'"
+	STRANDED='yes'
 fi
 
 echo -e "\nQuantifying expression, with strandedness: ${STRANDED}"
diff --git a/protocols/IndelRealignment.sh b/protocols/IndelRealignment.sh
index 246fa3a..80b5050 100755
--- a/protocols/IndelRealignment.sh
+++ b/protocols/IndelRealignment.sh
@@ -1,3 +1,4 @@
+set -o pipefail
 #MOLGENIS nodes=1 ppn=8 mem=11gb walltime=23:59:00
 
 #string project
diff --git a/protocols/Leafcutter.sh b/protocols/Leafcutter.sh
index ca6c5d6..276c903 100755
--- a/protocols/Leafcutter.sh
+++ b/protocols/Leafcutter.sh
@@ -1,3 +1,4 @@
+set -o pipefail
 #MOLGENIS nodes=1 ppn=1 mem=34gb walltime=05:00:00
 
 #Parameter mapping
@@ -22,10 +23,14 @@ module load "${python2Version}"
 module list
 
 # detect strand for RegTools
-STRANDED="$(num1="$(tail -n 2 "${strandedness}" | awk '{print $7}' | head -n 1)"; num2="$(tail -n 2 "${strandedness}" | awk '{print $7}' | tail -n 1)"; if (( $(echo "$num1 > 0.6" | bc -l) )); then echo "1"; fi; if (( $(echo "$num2 > 0.6" | bc -l) )); then echo "2"; fi; if (( $(echo "$num1 < 0.6 && $num2 < 0.6" | bc -l) )); then echo "0"; fi)"
+num1="$(tail -n 2 "${strandedness}" | awk '{print $7}' | head -n 1)"
+num2="$(tail -n 1 "${strandedness}" | awk '{print $7}')"
+
+STRANDED=$(echo -e "${num1}\t${num2}" | awk '{if ($1 > 0.6){print "1"}else if($2 > 0.6){print "2"}else if($1 < 0.6 && $2 < 0.6){print "0"} }')
 
 #detect number of conditions
-col=$(col="condition"; head -n1 "${projectJobsDir}/${project}.csv" | tr "," "\n" | grep -n $col)
+col=$(col="condition"; head -n1 "${projectJobsDir}/${project}.csv" | tr "," "\n" | grep -n "${col}")
+# shellcheck disable=SC2206
 colArray=(${col//:/ })
 conditionCount=$(tail -n +2 "${projectJobsDir}/${project}.csv" | cut -d "," -f "${colArray[0]}" | sort | uniq | wc -l)
 
@@ -33,9 +38,10 @@ echo -e "\nWith strandedness type: ${STRANDED},
 where (0 = unstranded, 1 = first-strand/RF, 2, = second-strand/FR)."
 
 echo "create group_list"
-col=$(col="externalSampleID"; head -n1 "${projectJobsDir}/${project}.csv" | tr "," "\n" | grep -n $col)
+col=$(col="externalSampleID"; head -n1 "${projectJobsDir}/${project}.csv" | tr "," "\n" | grep -n "${col}")
+# shellcheck disable=SC2206
 colID=(${col//:/ })
-awk -F',' -v id=${colID[0]} -v con=${colArray[0]} '{print $id".sorted.merged.bam\t"$con}' "${projectJobsDir}/${project}.csv" \
+awk -F',' -v id="${colID[0]}" -v con="${colArray[0]}" '{print ${id}".sorted.merged.bam\t"${con}}' "${projectJobsDir}/${project}.csv" \
 > "${intermediateDir}${project}_groups_file.txt"
 
 sed 1d "${intermediateDir}${project}_groups_file.txt" > "${intermediateDir}${project}"_groups_file.txt.tmp
diff --git a/protocols/Leafcutter_filter.sh b/protocols/Leafcutter_filter.sh
index b22b072..5adecba 100755
--- a/protocols/Leafcutter_filter.sh
+++ b/protocols/Leafcutter_filter.sh
@@ -1,3 +1,4 @@
+set -o pipefail
 #MOLGENIS nodes=1 ppn=1 mem=34gb walltime=05:00:00
 
 #Parameter mapping
diff --git a/protocols/Leafcutter_intron_clustering.sh b/protocols/Leafcutter_intron_clustering.sh
index bafb37c..4505c8e 100755
--- a/protocols/Leafcutter_intron_clustering.sh
+++ b/protocols/Leafcutter_intron_clustering.sh
@@ -1,3 +1,4 @@
+set -o pipefail
 #MOLGENIS nodes=1 ppn=1 mem=34gb walltime=05:00:00
 
 #Parameter mapping
@@ -16,12 +17,10 @@ module load "${python2Version}"
 module list
 
 # detect strand for RegTools
-STRANDED="$(num1="$(tail -n 2 "${strandedness}" | awk '{print $7}' | head -n 1)"; num2="$(tail -n 2 "${strandedness}" | awk '{print $7}' | tail -n 1)"; if (( $(echo "$num1 > 0.6" | bc -l) )); then echo "1"; fi; if (( $(echo "$num2 > 0.6" | bc -l) )); then echo "2"; fi; if (( $(echo "$num1 < 0.6 && $num2 < 0.6" | bc -l) )); then echo "0"; fi)"
+num1="$(tail -n 2 "${strandedness}" | awk '{print $7}' | head -n 1)"
+num2="$(tail -n 1 "${strandedness}" | awk '{print $7}')"
 
-#detect number of conditions
-col=$(col="condition"; head -n1 "${projectJobsDir}/${project}.csv" | tr "," "\n" | grep -n $col)
-colArray=(${col//:/ })
-conditionCount=$(tail -n +2 "${projectJobsDir}/${project}.csv" | cut -d "," -f "${colArray[0]}" | sort | uniq | wc -l)
+STRANDED=$(echo -e "${num1}\t${num2}" | awk '{if ($1 > 0.6){print "1"}else if($2 > 0.6){print "2"}else if($1 < 0.6 && $2 < 0.6){print "0"} }')
 
 echo -e "\nWith strandedness type: ${STRANDED},
 where (0 = unstranded, 1 = first-strand/RF, 2, = second-strand/FR)."
diff --git a/protocols/Leafcutter_rare.sh b/protocols/Leafcutter_rare.sh
index 223f36b..4288da1 100755
--- a/protocols/Leafcutter_rare.sh
+++ b/protocols/Leafcutter_rare.sh
@@ -1,3 +1,4 @@
+set -o pipefail
 #MOLGENIS nodes=1 ppn=1 mem=34gb walltime=05:00:00
 
 #Parameter mapping
diff --git a/protocols/MakeExpressionTable.sh b/protocols/MakeExpressionTable.sh
index 10aeb40..af53be9 100755
--- a/protocols/MakeExpressionTable.sh
+++ b/protocols/MakeExpressionTable.sh
@@ -1,3 +1,4 @@
+set -o pipefail
 #MOLGENIS walltime=24:00:00 nodes=1 cores=1 mem=2gb
 
 #string intermediateDir
diff --git a/protocols/MarkDuplicates.sh b/protocols/MarkDuplicates.sh
index 8ae64c1..ec68e75 100755
--- a/protocols/MarkDuplicates.sh
+++ b/protocols/MarkDuplicates.sh
@@ -1,3 +1,4 @@
+set -o pipefail
 #!/bin/bash
 #MOLGENIS walltime=23:59:00 mem=8gb ppn=6
 
diff --git a/protocols/MergeBam.sh b/protocols/MergeBam.sh
index 6c633e3..fa5f5c5 100755
--- a/protocols/MergeBam.sh
+++ b/protocols/MergeBam.sh
@@ -1,3 +1,4 @@
+set -o pipefail
 #MOLGENIS walltime=23:59:00 mem=8gb ppn=6
 
 #Parameter mapping
diff --git a/protocols/MultiQCReport.sh b/protocols/MultiQCReport.sh
index 557a0f8..08024b4 100755
--- a/protocols/MultiQCReport.sh
+++ b/protocols/MultiQCReport.sh
@@ -1,3 +1,4 @@
+set -o pipefail
 #MOLGENIS nodes=1 ppn=1 mem=5gb walltime=03:00:00
 
 #Parameter mapping
@@ -38,55 +39,54 @@
 cat > "${intermediateDir}/${project}_QC_config.yaml" <<'_EOF'
 
 report_header_info:
-  - 'Contact E-mail' : '${contact}'
-  - 'Pipeline Version' : '${ngsVersion}'
-  - 'Project' : '${project}'
-  - 'prepKit' : '${prepKit}'
-  - '' : ''
-  - 'Used toolversions' : ' '
-  - '' : ''
-  - '' : ${jdkVersion}
-  - '' : ${fastqcVersion}
-  - '' : ${starVersion}
-  - '' : ${samtoolsVersion}
-  - '' : ${rVersion}
-  - '' : ${wkhtmltopdfVersion}
-  - '' : ${picardVersion}
-  - '' : ${htseqVersion}
-  - '' : ${pythonVersion}
-  - '' : ${gatkVersion}
-  - '' : ${multiqcVersion}
-  - '' : ''
-  - 'pipeline description' : ''
-  - 'Gene expression quantification' : ''
-  - '' : 'The trimmed fastQ files where aligned to build ${indexFileID} reference genome using'
-  - '' : '${starVersion} [1] allowing for 2 mismatches. Before gene quantification'
-  - '' : '${samtoolsVersion} [2] was used to sort the aligned reads.'
-  - '' : 'The gene level quantification was performed by ${htseqVersion} [3] using --mode=union'
-  - '' : '--stranded=no and, Ensembl version 75 was used as gene annotation database which is included'
-  - '' : 'in folder expression/.'
-  - '' : ''
-  - 'QC metrics' : ''
-  - '' : 'Quality control (QC) metrics are calculated for the raw sequencing data. This is done using'
-  - '' : 'the tool FastQC FastQC [4]. QC metrics are calculated for the aligned reads using'
-  - '' : 'Picard-tools [5] CollectRnaSeqMetrics, MarkDuplicates, CollectInsertSize-'
-  - '' : 'Metrics and SAMtools flagstat.These QC metrics form the basis in this final QC report.'
-  - '' : ''
-  - 'references' : ''
-  - '' : ''
-  - '' : '1. Dobin A, Davis C a, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M,'
-  - '' : 'Gingeras TR: STAR: ultrafast universal RNA-seq aligner. Bioinformatics 2013, 29:15–21.'
-  - '' : '2. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R,'
-  - '' : 'Subgroup 1000 Genome Project Data Processing: The Sequence Alignment/Map format and SAMtools.'
-  - '' : 'Bioinforma 2009, 25 (16):2078–2079.'
-  - '' : '3. Anders S, Pyl PT, Huber W: HTSeq – A Python framework to work with high-throughput sequencing data'
-  - '' : 'HTSeq – A Python framework to work with high-throughput sequencing data. 2014:0–5.'
-  - '' : '4. Andrews, S. (2010). FastQC a Quality Control Tool for High Throughput Sequence Data [Online].'
-  - '' : 'Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ ${samtoolsVersion}'
-  - '' : '5. Picard Sourceforge Web site. http://picard.sourceforge.net/ ${picardVersion}'
+- 'Contact E-mail' : '${contact}'
+- 'Pipeline Version' : '${ngsVersion}'
+- 'Project' : '${project}'
+- 'prepKit' : '${prepKit}'
+- '' : ''
+- 'Used toolversions' : ' '
+- '' : ''
+- '' : ${jdkVersion}
+- '' : ${fastqcVersion}
+- '' : ${starVersion}
+- '' : ${samtoolsVersion}
+- '' : ${rVersion}
+- '' : ${wkhtmltopdfVersion}
+- '' : ${picardVersion}
+- '' : ${htseqVersion}
+- '' : ${pythonVersion}
+- '' : ${gatkVersion}
+- '' : ${multiqcVersion}
+- '' : ''
+- 'pipeline description' : ''
+- 'Gene expression quantification' : ''
+- '' : 'The trimmed fastQ files where aligned to build ${indexFileID} reference genome using'
+- '' : '${starVersion} [1] allowing for 2 mismatches. Before gene quantification'
+- '' : '${samtoolsVersion} [2] was used to sort the aligned reads.'
+- '' : 'The gene level quantification was performed by ${htseqVersion} [3] using --mode=union'
+- '' : '--stranded=no and, Ensembl version 75 was used as gene annotation database which is included'
+- '' : 'in folder expression/.'
+- '' : ''
+- 'QC metrics' : ''
+- '' : 'Quality control (QC) metrics are calculated for the raw sequencing data. This is done using'
+- '' : 'the tool FastQC FastQC [4]. QC metrics are calculated for the aligned reads using'
+- '' : 'Picard-tools [5] CollectRnaSeqMetrics, MarkDuplicates, CollectInsertSize-'
+- '' : 'Metrics and SAMtools flagstat.These QC metrics form the basis in this final QC report.'
+- '' : ''
+- 'references' : ''
+- '' : ''
+- '' : '1. Dobin A, Davis C a, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M,'
+- '' : 'Gingeras TR: STAR: ultrafast universal RNA-seq aligner. Bioinformatics 2013, 29:15–21.'
+- '' : '2. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R,'
+- '' : 'Subgroup 1000 Genome Project Data Processing: The Sequence Alignment/Map format and SAMtools.'
+- '' : 'Bioinforma 2009, 25 (16):2078–2079.'
+- '' : '3. Anders S, Pyl PT, Huber W: HTSeq – A Python framework to work with high-throughput sequencing data'
+- '' : 'HTSeq – A Python framework to work with high-throughput sequencing data. 2014:0–5.'
+- '' : '4. Andrews, S. (2010). FastQC a Quality Control Tool for High Throughput Sequence Data [Online].'
+- '' : 'Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ ${samtoolsVersion}'
+- '' : '5. Picard Sourceforge Web site. http://picard.sourceforge.net/ ${picardVersion}'
 _EOF
 
-
 # generate multiqc QC rapport
 
 singularity exec --bind "${intermediateDir}:/intermediateDir,${projectResultsDir}:/projectResultsDir" "${sifDir}${multiqcVersion}" \
diff --git a/protocols/OUTRIDER.sh b/protocols/OUTRIDER.sh
index d50cc5c..ff6dbfe 100755
--- a/protocols/OUTRIDER.sh
+++ b/protocols/OUTRIDER.sh
@@ -1,3 +1,4 @@
+set -o pipefail
 #MOLGENIS walltime=5:00:00 nodes=1 cores=1 mem=50gb
 
 #string intermediateDir
diff --git a/protocols/QCStats.sh b/protocols/QCStats.sh
index eb87b19..0dda1d9 100755
--- a/protocols/QCStats.sh
+++ b/protocols/QCStats.sh
@@ -1,3 +1,4 @@
+set -o pipefail
 #MOLGENIS nodes=1 ppn=1 mem=8gb walltime=05:59:00
 
 #Parameter mapping
@@ -41,7 +42,10 @@ module load "${ngsVersion}"
 module list
 
 # Get strandness.
-STRANDED="$(num1="$(tail -n 2 "${strandedness}" | awk '{print $7}' | head -n 1)"; num2="$(tail -n 2 "${strandedness}" | awk '{print $7}' | tail -n 1)"; if (( $(echo "$num1 > 0.6" | bc -l) )); then echo "SECOND_READ_TRANSCRIPTION_STRAND"; fi; if (( $(echo "$num2 > 0.6" | bc -l) )); then echo "FIRST_READ_TRANSCRIPTION_STRAND"; fi; if (( $(echo "$num1 < 0.6 && $num2 < 0.6" | bc -l) )); then echo "NONE"; fi)"
+num1="$(tail -n 2 "${strandedness}" | awk '{print $7}' | head -n 1)"
+num2="$(tail -n 1 "${strandedness}" | awk '{print $7}')"
+
+STRANDED=$(echo -e "${num1}\t${num2}" | awk '{if ($1 > 0.6){print "SECOND_READ_TRANSCRIPTION_STRAND"}else if($2 > 0.6){print "FIRST_READ_TRANSCRIPTION_STRAND"}else if($1 < 0.6 && $2 < 0.6){print "NONE"} }')
 
 #If paired-end do fastqc for both ends, else only for one
 if [[ "${seqType}" == "PE" ]]
diff --git a/protocols/RNASeQC.sh b/protocols/RNASeQC.sh
index a59105c..235b21a 100755
--- a/protocols/RNASeQC.sh
+++ b/protocols/RNASeQC.sh
@@ -1,3 +1,4 @@
+set -o pipefail
 #MOLGENIS walltime=5:59:00 mem=4gb ppn=1
 
 #Parameter mapping
diff --git a/protocols/RNASeQCPlots.sh b/protocols/RNASeQCPlots.sh
index fd16306..597db27 100755
--- a/protocols/RNASeQCPlots.sh
+++ b/protocols/RNASeQCPlots.sh
@@ -1,3 +1,4 @@
+set -o pipefail
 #MOLGENIS nodes=1 ppn=1 mem=1gb walltime=05:00:00
 
 #Parameter mapping
diff --git a/protocols/STAR.sh b/protocols/STAR.sh
index 16f7a2b..f098102 100755
--- a/protocols/STAR.sh
+++ b/protocols/STAR.sh
@@ -1,3 +1,4 @@
+set -o pipefail
 #MOLGENIS nodes=1 ppn=8 mem=40gb walltime=23:00:00
 
 #Parameter mapping
diff --git a/protocols/SplitAndTrim.sh b/protocols/SplitAndTrim.sh
index 93ee94a..ce9f759 100755
--- a/protocols/SplitAndTrim.sh
+++ b/protocols/SplitAndTrim.sh
@@ -1,3 +1,4 @@
+set -o pipefail
 #MOLGENIS nodes=1 ppn=2 mem=10gb walltime=23:59:00
 
 #string project
diff --git a/protocols/Stranded.sh b/protocols/Stranded.sh
index a285527..e850e45 100755
--- a/protocols/Stranded.sh
+++ b/protocols/Stranded.sh
@@ -1,3 +1,4 @@
+set -o pipefail
 #MOLGENIS nodes=1 ppn=1 mem=10gb walltime=05:00:00
 
 #Parameter mapping
diff --git a/protocols/TIN.sh b/protocols/TIN.sh
index b796d8d..b429729 100755
--- a/protocols/TIN.sh
+++ b/protocols/TIN.sh
@@ -1,3 +1,4 @@
+set -o pipefail
 #MOLGENIS walltime=23:59:00 mem=40gb ppn=1
 
 #Parameter mapping
diff --git a/protocols/TrimReads_TrimGalore.sh b/protocols/TrimReads_TrimGalore.sh
index d06b6b1..92c2e30 100755
--- a/protocols/TrimReads_TrimGalore.sh
+++ b/protocols/TrimReads_TrimGalore.sh
@@ -1,3 +1,4 @@
+set -o pipefail
 #MOLGENIS nodes=1 ppn=4 mem=4gb walltime=23:59:00
 
 #Parameter mapping
diff --git a/protocols/VIP.sh b/protocols/VIP.sh
index 253c26f..39f4fc1 100755
--- a/protocols/VIP.sh
+++ b/protocols/VIP.sh
@@ -1,3 +1,4 @@
+set -o pipefail
 #MOLGENIS walltime=05:59:00 mem=5gb ppn=1 nodes=1
 
 #string tmpTmpDataDir
@@ -16,27 +17,23 @@
 #string spliceaiIndel
 #string spliceaiSnv
 
-makeTmpDir "${projectBatchGenotypedVIPPrefix}"
-tmpProjectBatchGenotypedVIPPrefix=${MC_tmpFile}
-
 #Load modules
 module load "${vipVersion}"
 #Check modules
 module list
 
-	cp "$EBROOTVIP/config/default.cfg" "${intermediateDir}/vip.config"
+	cp "${EBROOTVIP}/config/default.cfg" "${intermediateDir}/vip.config"
 	echo "annotate_vep_plugin_SpliceAI=${spliceaiSnv},${spliceaiIndel}" >> "${intermediateDir}/vip.config"
 
-	echo "## "$(date)" Start $0"
-	cd "${EBROOTVIP}"
+	cd "${EBROOTVIP}" || exit
 	bash pipeline.sh \
 	-c "${intermediateDir}/vip.config" \
 	-i "${projectBatchGenotypedVariantCalls}" \
 	-o "${projectBatchGenotypedVIPPrefix}.vcf.gz"
-	cd -
+	cd - || exit
 	printf "VIP ..done\n"
 
-	cd "${intermediateDir}"
-	md5sum $(basename "${projectBatchGenotypedVIPPrefix}.vcf.gz")> $(basename "${projectBatchGenotypedVIPPrefix}.vcf.gz").md5
-	cd -
+	cd "${intermediateDir}" || exit
+	md5sum "$(basename "${projectBatchGenotypedVIPPrefix}.vcf.gz")" > "$(basename "${projectBatchGenotypedVIPPrefix}.vcf.gz").md5"
+	cd - || exit
 	echo "succes moving files"
diff --git a/protocols/annotate_SJ_with_SJDB.sh b/protocols/annotate_SJ_with_SJDB.sh
index 99b16e9..4734051 100755
--- a/protocols/annotate_SJ_with_SJDB.sh
+++ b/protocols/annotate_SJ_with_SJDB.sh
@@ -1,3 +1,4 @@
+set -o pipefail
 #MOLGENIS walltime=5:59:00 mem=4gb ppn=1
 
 #Parameter mapping
diff --git a/protocols/create_SJDB.sh b/protocols/create_SJDB.sh
index 4a5442f..f9b40b2 100755
--- a/protocols/create_SJDB.sh
+++ b/protocols/create_SJDB.sh
@@ -1,3 +1,4 @@
+set -o pipefail
 #MOLGENIS walltime=23:59:00 mem=4gb ppn=4
 
 #Parameter mapping
diff --git a/protocols/normalize_SJ.sh b/protocols/normalize_SJ.sh
index c15666c..71881df 100755
--- a/protocols/normalize_SJ.sh
+++ b/protocols/normalize_SJ.sh
@@ -1,3 +1,4 @@
+set -o pipefail
 #MOLGENIS walltime=23:59:00 mem=4gb ppn=1
 
 #Parameter mapping
diff --git a/protocols/rMATs.sh b/protocols/rMATs.sh
index 992cff6..0d723b6 100755
--- a/protocols/rMATs.sh
+++ b/protocols/rMATs.sh
@@ -1,3 +1,4 @@
+set -o pipefail
 #MOLGENIS walltime=23:59:00 mem=4gb ppn=4
 
 #Parameter mapping
@@ -41,8 +42,13 @@ do
 	echo "${status}"
 done < "${intermediateDir}${externalSampleID}.SJ.design.tsv"
 
+
 # Get strandness.
-STRANDED="$(num1="$(tail -n 2 "${strandedness}" | awk '{print $7}' | head -n 1)"; num2="$(tail -n 2 "${strandedness}" | awk '{print $7}' | tail -n 1)"; if (( $(echo "$num1 > 0.6" | bc -l) )); then echo "fr-secondstrand"; fi; if (( $(echo "$num2 > 0.6" | bc -l) )); then echo "fr-firststrand"; fi; if (( $(echo "$num1 < 0.6 && $num2 < 0.6" | bc -l) )); then echo "fr-unstranded"; fi)"
+
+num1="$(tail -n 2 "${strandedness}" | awk '{print $7}' | head -n 1)"
+num2="$(tail -n 1 "${strandedness}" | awk '{print $7}')"
+
+STRANDED=$(echo -e "${num1}\t${num2}" | awk '{if ($1 > 0.6){print "fr-secondstrand"}else if($2 > 0.6){print "fr-firststrand"}else if($1 < 0.6 && $2 < 0.6){print "fr-unstranded"} }')
 
 singularity exec --bind "${intermediateDir}":/intermediateDir,/apps:/apps,/groups:/groups "${sifDir}/${rMATsVersion}" python /rmats/rmats.py \
 --b1 "/intermediateDir/${externalSampleID}.B1.txt" --b2 "/intermediateDir/${externalSampleID}.B2.txt" \
diff --git a/protocols/rMats_reformat.sh b/protocols/rMats_reformat.sh
index 460a83f..cffd82f 100755
--- a/protocols/rMats_reformat.sh
+++ b/protocols/rMats_reformat.sh
@@ -1,3 +1,4 @@
+set -o pipefail
 #MOLGENIS walltime=23:59:00 mem=4gb ppn=4
 
 #Parameter mapping

From e4783525641906a5714824bdcdfd0e82a3cf781e Mon Sep 17 00:00:00 2001
From: gerbenvandervries <gerbenvandervries@gmail.com>
Date: Fri, 13 Jan 2023 11:48:35 +0000
Subject: [PATCH 13/42] removed unused tools, added gene name to ht_seq output

---
 parameters.gearshift.csv           |  1 +
 parameters.homo_sapiens.GRCh37.csv | 28 +++++++++++++---------------
 parameters.talos.csv               | 10 ++++++++++
 protocols/HTSeq_count.sh           |  1 +
 protocols/MultiQCReport.sh         |  3 ---
 protocols/QCStats.sh               |  1 -
 6 files changed, 25 insertions(+), 19 deletions(-)
 create mode 100755 parameters.talos.csv

diff --git a/parameters.gearshift.csv b/parameters.gearshift.csv
index 6f4ab1f..a300de9 100755
--- a/parameters.gearshift.csv
+++ b/parameters.gearshift.csv
@@ -7,3 +7,4 @@ root,/apps/
 tempDir,${workDir}/${tmpName}/tmp/
 permanentDir,${workDir}/prm03
 toolchain,foss-2018b
+GCCcoreVersion,GCCcore-7.3.0
diff --git a/parameters.homo_sapiens.GRCh37.csv b/parameters.homo_sapiens.GRCh37.csv
index b3b4dab..0531e74 100755
--- a/parameters.homo_sapiens.GRCh37.csv
+++ b/parameters.homo_sapiens.GRCh37.csv
@@ -4,36 +4,34 @@ checkStage,module list
 jobname,jobname
 
 ##### Tools and versions #####
-jdkVersion,Java/8-LTS
-ngsUtilsVersion,ngs-utils/19.03.3-GCCcore-7.3.0
+jdkVersion,Java/11-LTS
+ngsUtilsVersion,ngs-utils/19.03.3-${GCCcoreVersion}
 ngsRNAVersion,NGS_RNA/beta
 fastqcVersion,FastQC/0.11.8-Java-11-LTS
-samtoolsVersion,SAMtools/1.9-GCCcore-7.3.0
-bedToolsVersion,BEDTools/2.28.0-GCCcore-7.3.0
+samtoolsVersion,SAMtools/1.9-${GCCcoreVersion}
+bedToolsVersion,BEDTools/2.28.0-${GCCcoreVersion}
 sambambaVersion,sambamba/0.7.0
 rVersion,R/3.6.1-${toolchain}-bare
 rPlusVersion,RPlus/3.6.1-${toolchain}-v21.10.1
 picardVersion,picard/2.20.5-Java-11-LTS
-htseqVersion,HTSeq/0.11.0-GCCcore-7.3.0-Python-3.7.4
+htseqVersion,HTSeq/0.11.0-${GCCcoreVersion}-Python-3.7.4
 hisatVersion,hisat2/2.1.0-${toolchain}
-htsLibVersion,HTSlib/1.11-GCCcore-7.3.0
-pythonVersion,Python/3.7.4-GCCcore-7.3.0-bare
-python2Version,Python/2.7.16-GCCcore-7.3.0-bare
+htsLibVersion,HTSlib/1.11-${GCCcoreVersion}
+pythonVersion,Python/3.7.4-${GCCcoreVersion}-bare
+python2Version,Python/2.7.16-${GCCcoreVersion}-bare
 python2PlusVersion,PythonPlus/2.7.16-${toolchain}-v20.12.1
 pythonPlusVersion,PythonPlus/3.7.4-${toolchain}-v20.02.1
 gatkVersion,GATK/4.1.4.1-Java-8-LTS
 multiqcVersion,multiqc_v1.12.sif
-wkhtmltopdfVersion,wkhtmltopdf/0.11.0_rc1-static-amd64
-anacondaVersion,Anaconda/1.8.0-Linux-x86_64
 starVersion,STAR/2.7.3a-${toolchain}
 picardJar,picard.jar
 gatkJar,gatk-package-4.1.4.1-local.jar
 mergeSamFilesJar,MergeSamFiles
-trimGaloreVersion,TrimGalore/0.4.5-GCCcore-7.3.0-Python-3.7.4-bare
-cutadaptVersion,cutadapt/2.6-GCCcore-7.3.0-Python-3.7.4-bare
-rSeQCVersion,RSeQC/3.0.1-GCCcore-7.3.0-Python-3.7.4
-leafcutterVersion,leafcutter/aa12b1e-foss-2018b
-vipVersion,vip/v3.3.1-foss-2018b
+trimGaloreVersion,TrimGalore/0.4.5-${GCCcoreVersion}-Python-3.7.4-bare
+cutadaptVersion,cutadapt/2.6-${GCCcoreVersion}-Python-3.7.4-bare
+rSeQCVersion,RSeQC/3.0.1-${GCCcoreVersion}-Python-3.7.4
+leafcutterVersion,leafcutter/aa12b1e-${toolchain}
+vipVersion,vip/v3.3.1-${toolchain}
 outriderVersion,outrider_latest.sif
 rMATsVersion,rmats_v4.1.2.sif
 sifDir,/apps/data/GAD/singularity/
diff --git a/parameters.talos.csv b/parameters.talos.csv
new file mode 100755
index 0000000..3600453
--- /dev/null
+++ b/parameters.talos.csv
@@ -0,0 +1,10 @@
+#### ENVIRONMENT VARIABLES ####
+queue,atd
+workDir,/groups/${groupname}/
+dataDir,${root}/data/
+tmpName,tmp01
+root,/apps/
+tempDir,${workDir}/${tmpName}/tmp/
+permanentDir,${workDir}/prm08
+toolchain,foss-2022a
+GCCcoreVersion,GCCcore-11.3.0
diff --git a/protocols/HTSeq_count.sh b/protocols/HTSeq_count.sh
index b25ccc9..7e8ad2b 100755
--- a/protocols/HTSeq_count.sh
+++ b/protocols/HTSeq_count.sh
@@ -48,6 +48,7 @@ samtools \
 	htseq-count \
 	-m union \
 	-s "${STRANDED}" \
+	-i gene_name
 	- \
 	"${annotationGtf}" \
 	> "${tmpSampleHTseqExpressionText}"
diff --git a/protocols/MultiQCReport.sh b/protocols/MultiQCReport.sh
index 08024b4..e56718b 100755
--- a/protocols/MultiQCReport.sh
+++ b/protocols/MultiQCReport.sh
@@ -14,12 +14,10 @@ set -o pipefail
 #string gcPlotList
 #string seqType
 #string rVersion
-#string wkhtmltopdfVersion
 #string fastqcVersion
 #string samtoolsVersion
 #string picardVersion
 #string multiqcVersion
-#string anacondaVersion
 #string starVersion
 #string indexFileID
 #string ensembleReleaseVersion
@@ -51,7 +49,6 @@ report_header_info:
 - '' : ${starVersion}
 - '' : ${samtoolsVersion}
 - '' : ${rVersion}
-- '' : ${wkhtmltopdfVersion}
 - '' : ${picardVersion}
 - '' : ${htseqVersion}
 - '' : ${pythonVersion}
diff --git a/protocols/QCStats.sh b/protocols/QCStats.sh
index 0dda1d9..14f64b1 100755
--- a/protocols/QCStats.sh
+++ b/protocols/QCStats.sh
@@ -23,7 +23,6 @@ set -o pipefail
 #string alignmentMetrics
 #string externalSampleID
 #string picardVersion
-#string anacondaVersion
 #string samtoolsVersion
 #string ngsVersion
 #string pythonVersion

From 9972d1f9c9628b8fa0ac75e94a1f959ce0425914 Mon Sep 17 00:00:00 2001
From: gerbenvandervries <gerbenvandervries@gmail.com>
Date: Fri, 13 Jan 2023 11:52:58 +0000
Subject: [PATCH 14/42] .

---
 parameters.homo_sapiens.GRCh37.solve-rd.csv | 30 ++++++++++-----------
 1 file changed, 14 insertions(+), 16 deletions(-)

diff --git a/parameters.homo_sapiens.GRCh37.solve-rd.csv b/parameters.homo_sapiens.GRCh37.solve-rd.csv
index bfe8680..47ea2dd 100755
--- a/parameters.homo_sapiens.GRCh37.solve-rd.csv
+++ b/parameters.homo_sapiens.GRCh37.solve-rd.csv
@@ -4,39 +4,37 @@ checkStage,module list
 jobname,jobname
 
 ##### Tools and versions #####
-jdkVersion,Java/8-LTS
-ngsUtilsVersion,ngs-utils/19.03.3-GCCcore-7.3.0
+jdkVersion,Java/11-LTS
+ngsUtilsVersion,ngs-utils/19.03.3-${GCCcoreVersion}
 ngsRNAVersion,NGS_RNA/beta
 fastqcVersion,FastQC/0.11.8-Java-11-LTS
-samtoolsVersion,SAMtools/1.9-GCCcore-7.3.0
-bedToolsVersion,BEDTools/2.28.0-GCCcore-7.3.0
+samtoolsVersion,SAMtools/1.9-${GCCcoreVersion}
+bedToolsVersion,BEDTools/2.28.0-${GCCcoreVersion}
 sambambaVersion,sambamba/0.7.0
 rVersion,R/3.6.1-${toolchain}-bare
 rPlusVersion,RPlus/3.6.1-${toolchain}-v21.10.1
 picardVersion,picard/2.20.5-Java-11-LTS
-htseqVersion,HTSeq/0.11.0-GCCcore-7.3.0-Python-3.7.4
+htseqVersion,HTSeq/0.11.0-${GCCcoreVersion}-Python-3.7.4
 hisatVersion,hisat2/2.1.0-${toolchain}
-htsLibVersion,HTSlib/1.11-GCCcore-7.3.0
-pythonVersion,Python/3.7.4-GCCcore-7.3.0-bare
-python2Version,Python/2.7.16-GCCcore-7.3.0-bare
+htsLibVersion,HTSlib/1.11-${GCCcoreVersion}
+pythonVersion,Python/3.7.4-${GCCcoreVersion}-bare
+python2Version,Python/2.7.16-${GCCcoreVersion}-bare
 python2PlusVersion,PythonPlus/2.7.16-${toolchain}-v20.12.1
 pythonPlusVersion,PythonPlus/3.7.4-${toolchain}-v20.02.1
 gatkVersion,GATK/4.1.4.1-Java-8-LTS
 multiqcVersion,multiqc_v1.12.sif
-wkhtmltopdfVersion,wkhtmltopdf/0.11.0_rc1-static-amd64
-anacondaVersion,Anaconda/1.8.0-Linux-x86_64
 starVersion,STAR/2.7.3a-${toolchain}
 picardJar,picard.jar
 gatkJar,gatk-package-4.1.4.1-local.jar
 mergeSamFilesJar,MergeSamFiles
-trimGaloreVersion,TrimGalore/0.4.5-GCCcore-7.3.0-Python-3.7.4-bare
-cutadaptVersion,cutadapt/2.6-GCCcore-7.3.0-Python-3.7.4-bare
-rSeQCVersion,RSeQC/3.0.1-GCCcore-7.3.0-Python-3.7.4
-leafcutterVersion,leafcutter/aa12b1e-foss-2018b
-vipVersion,vip/v3.3.1-foss-2018b
+trimGaloreVersion,TrimGalore/0.4.5-${GCCcoreVersion}-Python-3.7.4-bare
+cutadaptVersion,cutadapt/2.6-${GCCcoreVersion}-Python-3.7.4-bare
+rSeQCVersion,RSeQC/3.0.1-${GCCcoreVersion}-Python-3.7.4
+leafcutterVersion,leafcutter/aa12b1e-${toolchain}
+vipVersion,vip/v3.3.1-${toolchain}
 outriderVersion,outrider_latest.sif
 rMATsVersion,rmats_v4.1.2.sif
-sifDir,/groups/umcg-solve-rd/tmp01/resources/GAD/singularity/
+sifDir,/apps/data/GAD/singularity/
 rnaseqcVersion,${sifDir}/rnaseqc_2.4.2.sif
 
 ##### GENERAL DIRECTORIES #####

From 4d3c4d2e3dbfbfc75723eb6e0349ef5c701c94de Mon Sep 17 00:00:00 2001
From: gerbenvandervries <gerbenvandervries@gmail.com>
Date: Fri, 13 Jan 2023 11:53:23 +0000
Subject: [PATCH 15/42] new parameters

---
 parameters.homo_sapiens.hg19.solve-rd.csv | 30 +++++++++++------------
 1 file changed, 14 insertions(+), 16 deletions(-)

diff --git a/parameters.homo_sapiens.hg19.solve-rd.csv b/parameters.homo_sapiens.hg19.solve-rd.csv
index d7b4b65..160036a 100755
--- a/parameters.homo_sapiens.hg19.solve-rd.csv
+++ b/parameters.homo_sapiens.hg19.solve-rd.csv
@@ -4,39 +4,37 @@ checkStage,module list
 jobname,jobname
 
 ##### Tools and versions #####
-jdkVersion,Java/8-LTS
-ngsUtilsVersion,ngs-utils/19.03.3-GCCcore-7.3.0
+jdkVersion,Java/11-LTS
+ngsUtilsVersion,ngs-utils/19.03.3-${GCCcoreVersion}
 ngsRNAVersion,NGS_RNA/beta
 fastqcVersion,FastQC/0.11.8-Java-11-LTS
-samtoolsVersion,SAMtools/1.9-GCCcore-7.3.0
-bedToolsVersion,BEDTools/2.28.0-GCCcore-7.3.0
+samtoolsVersion,SAMtools/1.9-${GCCcoreVersion}
+bedToolsVersion,BEDTools/2.28.0-${GCCcoreVersion}
 sambambaVersion,sambamba/0.7.0
 rVersion,R/3.6.1-${toolchain}-bare
 rPlusVersion,RPlus/3.6.1-${toolchain}-v21.10.1
 picardVersion,picard/2.20.5-Java-11-LTS
-htseqVersion,HTSeq/0.11.0-GCCcore-7.3.0-Python-3.7.4
+htseqVersion,HTSeq/0.11.0-${GCCcoreVersion}-Python-3.7.4
 hisatVersion,hisat2/2.1.0-${toolchain}
-htsLibVersion,HTSlib/1.11-GCCcore-7.3.0
-pythonVersion,Python/3.7.4-GCCcore-7.3.0-bare
-python2Version,Python/2.7.16-GCCcore-7.3.0-bare
+htsLibVersion,HTSlib/1.11-${GCCcoreVersion}
+pythonVersion,Python/3.7.4-${GCCcoreVersion}-bare
+python2Version,Python/2.7.16-${GCCcoreVersion}-bare
 python2PlusVersion,PythonPlus/2.7.16-${toolchain}-v20.12.1
 pythonPlusVersion,PythonPlus/3.7.4-${toolchain}-v20.02.1
 gatkVersion,GATK/4.1.4.1-Java-8-LTS
 multiqcVersion,multiqc_v1.12.sif
-wkhtmltopdfVersion,wkhtmltopdf/0.11.0_rc1-static-amd64
-anacondaVersion,Anaconda/1.8.0-Linux-x86_64
 starVersion,STAR/2.7.3a-${toolchain}
 picardJar,picard.jar
 gatkJar,gatk-package-4.1.4.1-local.jar
 mergeSamFilesJar,MergeSamFiles
-trimGaloreVersion,TrimGalore/0.4.5-GCCcore-7.3.0-Python-3.7.4-bare
-cutadaptVersion,cutadapt/2.6-GCCcore-7.3.0-Python-3.7.4-bare
-rSeQCVersion,RSeQC/3.0.1-GCCcore-7.3.0-Python-3.7.4
-leafcutterVersion,leafcutter/aa12b1e-foss-2018b
-vipVersion,vip/v3.3.1-foss-2018b
+trimGaloreVersion,TrimGalore/0.4.5-${GCCcoreVersion}-Python-3.7.4-bare
+cutadaptVersion,cutadapt/2.6-${GCCcoreVersion}-Python-3.7.4-bare
+rSeQCVersion,RSeQC/3.0.1-${GCCcoreVersion}-Python-3.7.4
+leafcutterVersion,leafcutter/aa12b1e-${toolchain}
+vipVersion,vip/v3.3.1-${toolchain}
 outriderVersion,outrider_latest.sif
 rMATsVersion,rmats_v4.1.2.sif
-sifDir,/groups/umcg-solve-rd/tmp01/resources/GAD/singularity/
+sifDir,/apps/data/GAD/singularity/
 rnaseqcVersion,${sifDir}/rnaseqc_2.4.2.sif
 
 ##### GENERAL DIRECTORIES #####

From 0a2cfb802fcb51097de911f9247ab94cf08cb589 Mon Sep 17 00:00:00 2001
From: gerbenvandervries <gerbenvandervries@gmail.com>
Date: Thu, 12 Jan 2023 13:03:04 +0100
Subject: [PATCH 16/42] bugfixes

---
 protocols/BQSR.sh       | 2 +-
 protocols/Leafcutter.sh | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/protocols/BQSR.sh b/protocols/BQSR.sh
index eba2f22..4c1cbce 100755
--- a/protocols/BQSR.sh
+++ b/protocols/BQSR.sh
@@ -36,7 +36,7 @@ module list
 echo "Running GATK BQSR:"
 
 
-jan -jar -Xmx7g -XX:ParallelGCThreads=2 -Djava.io.tmpdir="${tmpTmpDataDir}" \
+java -jar -Xmx7g -XX:ParallelGCThreads=2 -Djava.io.tmpdir="${tmpTmpDataDir}" \
 "${EBROOTGATK}/gatk-package-4.1.4.1-local.jar" BaseRecalibrator \
 -R "${indexFile}" \
 -I "${splitAndTrimBam}" \
diff --git a/protocols/Leafcutter.sh b/protocols/Leafcutter.sh
index 276c903..b672fb1 100755
--- a/protocols/Leafcutter.sh
+++ b/protocols/Leafcutter.sh
@@ -41,7 +41,7 @@ echo "create group_list"
 col=$(col="externalSampleID"; head -n1 "${projectJobsDir}/${project}.csv" | tr "," "\n" | grep -n "${col}")
 # shellcheck disable=SC2206
 colID=(${col//:/ })
-awk -F',' -v id="${colID[0]}" -v con="${colArray[0]}" '{print ${id}".sorted.merged.bam\t"${con}}' "${projectJobsDir}/${project}.csv" \
+awk -F',' -v id="${colID[0]}" -v con="${colArray[0]}" '{print ${id}".sorted.merged.bam\t"$con}' "${projectJobsDir}/${project}.csv" \
 > "${intermediateDir}${project}_groups_file.txt"
 
 sed 1d "${intermediateDir}${project}_groups_file.txt" > "${intermediateDir}${project}"_groups_file.txt.tmp

From 7df5f78e4a307e086db0940701b0489f7c8d4c79 Mon Sep 17 00:00:00 2001
From: gerbenvandervries <gerbenvandervries@gmail.com>
Date: Fri, 13 Jan 2023 12:34:24 +0000
Subject: [PATCH 17/42] removed unused tool

---
 protocols/CopyToResultsDir.sh | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/protocols/CopyToResultsDir.sh b/protocols/CopyToResultsDir.sh
index 8ee5487..7b50f4a 100755
--- a/protocols/CopyToResultsDir.sh
+++ b/protocols/CopyToResultsDir.sh
@@ -19,7 +19,6 @@ set -o pipefail
 #string fastqcVersion
 #string samtoolsVersion
 #string rVersion
-#string wkhtmltopdfVersion
 #string picardVersion
 #string starVersion
 #string htseqVersion
@@ -38,10 +37,6 @@ set -o pipefail
 #string tmpName
 #string logsDir
 
-# Change permissions
-
-umask 0007
-
 # Make result directories
 mkdir -p "${projectResultsDir}/alignment"
 mkdir -p "${projectResultsDir}/fastqc"

From 594abf897d91b20b26103c26a1f8f1ab82f2c3e7 Mon Sep 17 00:00:00 2001
From: gerbenvandervries <gerbenvandervries@gmail.com>
Date: Fri, 13 Jan 2023 15:59:53 +0000
Subject: [PATCH 18/42] fix for getting the correct gene_name out of a GTF

---
 scripts/annotate_SJ_with_genes.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/scripts/annotate_SJ_with_genes.py b/scripts/annotate_SJ_with_genes.py
index 407864e..58c2cef 100755
--- a/scripts/annotate_SJ_with_genes.py
+++ b/scripts/annotate_SJ_with_genes.py
@@ -38,9 +38,12 @@
         continue
     line = line.strip()
     tabs = line.split('\t')
+    arr_genetotal = line.split('"')
     gene = line.split('"')[1]
     chrm, start, end = tabs[0], int(tabs[3]), int(tabs[4])
-    gene = line.split('"')[1]
+    # get col number of 'gene_name' in arr_genetotal, add 1 to it \ 
+    # to get the actual 'gene_name value' from the next array value.
+    gene = line.split('"')[arr_genetotal.index("; gene_name ")+1]
     if gene not in genes_dict:
         genes_dict[gene] = [chrm, start, end]
     elif chrm == genes_dict[gene][0]:

From b0df409c0cf921a74a6e253782db0af17e8315ad Mon Sep 17 00:00:00 2001
From: gerbenvandervries <gerbenvandervries@gmail.com>
Date: Tue, 17 Jan 2023 12:24:16 +0000
Subject: [PATCH 19/42] bugs

---
 protocols/HTSeq_count.sh | 2 +-
 protocols/Leafcutter.sh  | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/protocols/HTSeq_count.sh b/protocols/HTSeq_count.sh
index 7e8ad2b..04e0478 100755
--- a/protocols/HTSeq_count.sh
+++ b/protocols/HTSeq_count.sh
@@ -48,7 +48,7 @@ samtools \
 	htseq-count \
 	-m union \
 	-s "${STRANDED}" \
-	-i gene_name
+	-i gene_name \
 	- \
 	"${annotationGtf}" \
 	> "${tmpSampleHTseqExpressionText}"
diff --git a/protocols/Leafcutter.sh b/protocols/Leafcutter.sh
index b672fb1..f94158f 100755
--- a/protocols/Leafcutter.sh
+++ b/protocols/Leafcutter.sh
@@ -41,7 +41,7 @@ echo "create group_list"
 col=$(col="externalSampleID"; head -n1 "${projectJobsDir}/${project}.csv" | tr "," "\n" | grep -n "${col}")
 # shellcheck disable=SC2206
 colID=(${col//:/ })
-awk -F',' -v id="${colID[0]}" -v con="${colArray[0]}" '{print ${id}".sorted.merged.bam\t"$con}' "${projectJobsDir}/${project}.csv" \
+awk -F',' -v id="${colID[0]}" -v con="${colArray[0]}" '{print $id".sorted.merged.bam\t"$con}' "${projectJobsDir}/${project}.csv" \
 > "${intermediateDir}${project}_groups_file.txt"
 
 sed 1d "${intermediateDir}${project}_groups_file.txt" > "${intermediateDir}${project}"_groups_file.txt.tmp

From 218d3e85f3d468a9eaf0e9852df94f5053bf478a Mon Sep 17 00:00:00 2001
From: gerbenvandervries <gerbenvandervries@gmail.com>
Date: Fri, 20 Jan 2023 12:13:14 +0000
Subject: [PATCH 20/42] added hc parameters, and moved toolVersions to host
 params

---
 parameters.gearshift.csv                    | 34 ++++++++++++++++
 parameters.homo_sapiens.GRCh37.csv          | 36 +----------------
 parameters.homo_sapiens.GRCh37.solve-rd.csv | 35 +---------------
 parameters.hyperchicken.csv                 | 44 +++++++++++++++++++++
 4 files changed, 80 insertions(+), 69 deletions(-)
 create mode 100755 parameters.hyperchicken.csv

diff --git a/parameters.gearshift.csv b/parameters.gearshift.csv
index a300de9..abf8467 100755
--- a/parameters.gearshift.csv
+++ b/parameters.gearshift.csv
@@ -8,3 +8,37 @@ tempDir,${workDir}/${tmpName}/tmp/
 permanentDir,${workDir}/prm03
 toolchain,foss-2018b
 GCCcoreVersion,GCCcore-7.3.0
+
+##### Tools and versions #####
+jdkVersion,Java/11-LTS
+ngsUtilsVersion,ngs-utils/19.03.3-${GCCcoreVersion}
+ngsRNAVersion,NGS_RNA/beta
+fastqcVersion,FastQC/0.11.8-Java-11-LTS
+samtoolsVersion,SAMtools/1.9-${GCCcoreVersion}
+bedToolsVersion,BEDTools/2.28.0-${GCCcoreVersion}
+sambambaVersion,sambamba/0.7.0
+rVersion,R/3.6.1-${toolchain}-bare
+rPlusVersion,RPlus/3.6.1-${toolchain}-v21.10.1
+picardVersion,picard/2.20.5-Java-11-LTS
+htseqVersion,HTSeq/0.11.0-${GCCcoreVersion}-Python-3.7.4
+hisatVersion,hisat2/2.1.0-${toolchain}
+htsLibVersion,HTSlib/1.11-${GCCcoreVersion}
+pythonVersion,Python/3.7.4-${GCCcoreVersion}-bare
+python2Version,Python/2.7.16-${GCCcoreVersion}-bare
+python2PlusVersion,PythonPlus/2.7.16-${toolchain}-v20.12.1
+pythonPlusVersion,PythonPlus/3.7.4-${toolchain}-v20.02.1
+gatkVersion,GATK/4.1.4.1-Java-8-LTS
+multiqcVersion,multiqc_v1.12.sif
+starVersion,STAR/2.7.3a-${toolchain}
+picardJar,picard.jar
+gatkJar,gatk-package-4.1.4.1-local.jar
+mergeSamFilesJar,MergeSamFiles
+trimGaloreVersion,TrimGalore/0.4.5-${GCCcoreVersion}-Python-3.7.4-bare
+cutadaptVersion,cutadapt/2.6-${GCCcoreVersion}-Python-3.7.4-bare
+rSeQCVersion,RSeQC/3.0.1-${GCCcoreVersion}-Python-3.7.4
+leafcutterVersion,leafcutter/aa12b1e-${toolchain}
+vipVersion,vip/v3.3.1-${toolchain}
+outriderVersion,outrider_latest.sif
+rMATsVersion,rmats_v4.1.2.sif
+sifDir,/apps/data/GAD/singularity/
+rnaseqcVersion,${sifDir}/rnaseqc_2.4.2.sif
diff --git a/parameters.homo_sapiens.GRCh37.csv b/parameters.homo_sapiens.GRCh37.csv
index 0531e74..07ad53b 100755
--- a/parameters.homo_sapiens.GRCh37.csv
+++ b/parameters.homo_sapiens.GRCh37.csv
@@ -3,40 +3,6 @@ stage,module load
 checkStage,module list
 jobname,jobname
 
-##### Tools and versions #####
-jdkVersion,Java/11-LTS
-ngsUtilsVersion,ngs-utils/19.03.3-${GCCcoreVersion}
-ngsRNAVersion,NGS_RNA/beta
-fastqcVersion,FastQC/0.11.8-Java-11-LTS
-samtoolsVersion,SAMtools/1.9-${GCCcoreVersion}
-bedToolsVersion,BEDTools/2.28.0-${GCCcoreVersion}
-sambambaVersion,sambamba/0.7.0
-rVersion,R/3.6.1-${toolchain}-bare
-rPlusVersion,RPlus/3.6.1-${toolchain}-v21.10.1
-picardVersion,picard/2.20.5-Java-11-LTS
-htseqVersion,HTSeq/0.11.0-${GCCcoreVersion}-Python-3.7.4
-hisatVersion,hisat2/2.1.0-${toolchain}
-htsLibVersion,HTSlib/1.11-${GCCcoreVersion}
-pythonVersion,Python/3.7.4-${GCCcoreVersion}-bare
-python2Version,Python/2.7.16-${GCCcoreVersion}-bare
-python2PlusVersion,PythonPlus/2.7.16-${toolchain}-v20.12.1
-pythonPlusVersion,PythonPlus/3.7.4-${toolchain}-v20.02.1
-gatkVersion,GATK/4.1.4.1-Java-8-LTS
-multiqcVersion,multiqc_v1.12.sif
-starVersion,STAR/2.7.3a-${toolchain}
-picardJar,picard.jar
-gatkJar,gatk-package-4.1.4.1-local.jar
-mergeSamFilesJar,MergeSamFiles
-trimGaloreVersion,TrimGalore/0.4.5-${GCCcoreVersion}-Python-3.7.4-bare
-cutadaptVersion,cutadapt/2.6-${GCCcoreVersion}-Python-3.7.4-bare
-rSeQCVersion,RSeQC/3.0.1-${GCCcoreVersion}-Python-3.7.4
-leafcutterVersion,leafcutter/aa12b1e-${toolchain}
-vipVersion,vip/v3.3.1-${toolchain}
-outriderVersion,outrider_latest.sif
-rMATsVersion,rmats_v4.1.2.sif
-sifDir,/apps/data/GAD/singularity/
-rnaseqcVersion,${sifDir}/rnaseqc_2.4.2.sif
-
 ##### GENERAL DIRECTORIES #####
 tmpDataDir,${workDir}/${tmpName}/
 tmpTmpDataDir,${tmpDataDir}/tmp/
@@ -164,7 +130,7 @@ gtexJunc,/apps/data/GAD/others/GTEx_v7_bflb_junctions.gct
 omimList,/apps/data/GAD/others/OMIM2.list
 indexFile,${indexSpecies}
 dbsnpVcf,/apps/data/dbSNP/dbsnp_137.b37.vcf
-starIndex,/apps/data/Ensembl/GrCh37.75/pub/release-75/fasta/homo_sapiens/STAR-2.7.3a-foss-2018b/
+starIndex,/apps/data/Ensembl/GrCh37.75/pub/release-75/fasta/homo_sapiens/STAR-2.7.3a-${GCCcoreVersion}/
 #### GENOME VARIABLES ####
 genome,GRCh37
 ensembleReleaseVersion,75
diff --git a/parameters.homo_sapiens.GRCh37.solve-rd.csv b/parameters.homo_sapiens.GRCh37.solve-rd.csv
index 47ea2dd..1b403ad 100755
--- a/parameters.homo_sapiens.GRCh37.solve-rd.csv
+++ b/parameters.homo_sapiens.GRCh37.solve-rd.csv
@@ -3,40 +3,6 @@ stage,module load
 checkStage,module list
 jobname,jobname
 
-##### Tools and versions #####
-jdkVersion,Java/11-LTS
-ngsUtilsVersion,ngs-utils/19.03.3-${GCCcoreVersion}
-ngsRNAVersion,NGS_RNA/beta
-fastqcVersion,FastQC/0.11.8-Java-11-LTS
-samtoolsVersion,SAMtools/1.9-${GCCcoreVersion}
-bedToolsVersion,BEDTools/2.28.0-${GCCcoreVersion}
-sambambaVersion,sambamba/0.7.0
-rVersion,R/3.6.1-${toolchain}-bare
-rPlusVersion,RPlus/3.6.1-${toolchain}-v21.10.1
-picardVersion,picard/2.20.5-Java-11-LTS
-htseqVersion,HTSeq/0.11.0-${GCCcoreVersion}-Python-3.7.4
-hisatVersion,hisat2/2.1.0-${toolchain}
-htsLibVersion,HTSlib/1.11-${GCCcoreVersion}
-pythonVersion,Python/3.7.4-${GCCcoreVersion}-bare
-python2Version,Python/2.7.16-${GCCcoreVersion}-bare
-python2PlusVersion,PythonPlus/2.7.16-${toolchain}-v20.12.1
-pythonPlusVersion,PythonPlus/3.7.4-${toolchain}-v20.02.1
-gatkVersion,GATK/4.1.4.1-Java-8-LTS
-multiqcVersion,multiqc_v1.12.sif
-starVersion,STAR/2.7.3a-${toolchain}
-picardJar,picard.jar
-gatkJar,gatk-package-4.1.4.1-local.jar
-mergeSamFilesJar,MergeSamFiles
-trimGaloreVersion,TrimGalore/0.4.5-${GCCcoreVersion}-Python-3.7.4-bare
-cutadaptVersion,cutadapt/2.6-${GCCcoreVersion}-Python-3.7.4-bare
-rSeQCVersion,RSeQC/3.0.1-${GCCcoreVersion}-Python-3.7.4
-leafcutterVersion,leafcutter/aa12b1e-${toolchain}
-vipVersion,vip/v3.3.1-${toolchain}
-outriderVersion,outrider_latest.sif
-rMATsVersion,rmats_v4.1.2.sif
-sifDir,/apps/data/GAD/singularity/
-rnaseqcVersion,${sifDir}/rnaseqc_2.4.2.sif
-
 ##### GENERAL DIRECTORIES #####
 tmpDataDir,/groups/umcg-solve-rd/tmp01/rna/
 tmpTmpDataDir,/groups/umcg-solve-rd/tmp01/rna/tmp/
@@ -186,3 +152,4 @@ annotationFile,${dataDir}Ensembl/GrCh37.75/pub/release-75/gtf/${speciesFileName}
 ensembleDir,${dataDir}/ftp.broadinstitute.org/bundle/2.8/${genome}/gtf/${speciesFileName}/
 spliceaiSnv,/apps/data/SpliceAI/GRCh37/spliceai_scores.raw.snv.vcf.gz
 spliceaiIndel,/apps/data/SpliceAI/GRCh37/spliceai_scores.raw.indel.vcf.gz
+leafcutterAllExon,/apps/data/GAD/others/gencode_GRCh37_all_exons.txt.gz
diff --git a/parameters.hyperchicken.csv b/parameters.hyperchicken.csv
new file mode 100755
index 0000000..0c0ab32
--- /dev/null
+++ b/parameters.hyperchicken.csv
@@ -0,0 +1,44 @@
+#### ENVIRONMENT VARIABLES ####
+queue,atd
+workDir,/groups/${groupname}/
+dataDir,${root}/data/
+tmpName,tmp01
+root,/apps/
+tempDir,${workDir}/${tmpName}/tmp/
+permanentDir,${workDir}/prm03
+toolchain,foss-2022a
+GCCcoreVersion,GCCcore-11.3.0
+
+##### Tools and versions #####
+jdkVersion,Java/11-LTS
+ngsUtilsVersion,ngs-utils/19.03.3-${GCCcoreVersion}
+ngsRNAVersion,NGS_RNA/beta
+fastqcVersion,FastQC/0.11.8-Java-11-LTS
+samtoolsVersion,SAMtools/1.16.1-${GCCcoreVersion}
+bedToolsVersion,BEDTools/2.30.0-${GCCcoreVersion}
+sambambaVersion,sambamba/0.7.0
+rVersion,R/4.2.1-${toolchain}-bare
+rPlusVersion,RPlus/4.2.1-${toolchain}-v21.10.1
+picardVersion,picard/2.26.10-Java-8-LTS
+htseqVersion,HTSeq/0.11.0-${GCCcoreVersion}-Python-3.10.4
+hisatVersion,hisat2/2.1.0-${toolchain}
+htsLibVersion,HTSlib/1.16-${GCCcoreVersion}
+pythonVersion,Python/3.10.4-${GCCcoreVersion}-bare
+python2Version,Python/2.7.16-${GCCcoreVersion}-bare
+python2PlusVersion,PythonPlus/2.7.16-${toolchain}-v20.12.1
+pythonPlusVersion,PythonPlus/3.10.4-${toolchain}-v22.11.3
+gatkVersion,GATK/4.1.4.1-Java-8-LTS
+multiqcVersion,multiqc_v1.12.sif
+starVersion,STAR/2.7.3a-${toolchain}
+picardJar,picard.jar
+gatkJar,gatk-package-4.1.4.1-local.jar
+mergeSamFilesJar,MergeSamFiles
+trimGaloreVersion,TrimGalore/0.4.5-${GCCcoreVersion}-Python-3.10.4-bare
+cutadaptVersion,cutadapt/2.6-${GCCcoreVersion}-Python-3.10.4-bare
+rSeQCVersion,RSeQC/3.0.1-${GCCcoreVersion}-Python-3.10.4
+leafcutterVersion,leafcutter/aa12b1e-${toolchain}
+vipVersion,vip/v3.3.1-${toolchain}
+outriderVersion,outrider_latest.sif
+rMATsVersion,rmats_v4.1.2.sif
+sifDir,/apps/data/GAD/singularity/
+rnaseqcVersion,${sifDir}/rnaseqc_2.4.2.sif

From 655b31b43d573b8d4da1dbf8747989f88ece80b5 Mon Sep 17 00:00:00 2001
From: gerbenvandervries <gerbenvandervries@gmail.com>
Date: Wed, 1 Feb 2023 09:20:58 +0000
Subject: [PATCH 21/42] versions update

---
 parameters.hyperchicken.csv | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/parameters.hyperchicken.csv b/parameters.hyperchicken.csv
index 0c0ab32..9e47809 100755
--- a/parameters.hyperchicken.csv
+++ b/parameters.hyperchicken.csv
@@ -34,7 +34,7 @@ picardJar,picard.jar
 gatkJar,gatk-package-4.1.4.1-local.jar
 mergeSamFilesJar,MergeSamFiles
 trimGaloreVersion,TrimGalore/0.4.5-${GCCcoreVersion}-Python-3.10.4-bare
-cutadaptVersion,cutadapt/2.6-${GCCcoreVersion}-Python-3.10.4-bare
+cutadaptVersion,cutadapt/4.2-${GCCcoreVersion}-Python-3.10.4-bare
 rSeQCVersion,RSeQC/3.0.1-${GCCcoreVersion}-Python-3.10.4
 leafcutterVersion,leafcutter/aa12b1e-${toolchain}
 vipVersion,vip/v3.3.1-${toolchain}

From d2336abb04dbc71c07d7b35837371ec96a8e0fa6 Mon Sep 17 00:00:00 2001
From: gerbenvandervries <gerbenvandervries@gmail.com>
Date: Thu, 2 Feb 2023 07:51:35 +0000
Subject: [PATCH 22/42] fix hostparams

---
 parameters.fender.csv    | 35 +++++++++++++++++++++++++++++++++++
 parameters.gearshift.csv |  2 +-
 parameters.talos.csv     | 34 ++++++++++++++++++++++++++++++++++
 3 files changed, 70 insertions(+), 1 deletion(-)

diff --git a/parameters.fender.csv b/parameters.fender.csv
index c4e5c48..5c32e60 100755
--- a/parameters.fender.csv
+++ b/parameters.fender.csv
@@ -7,3 +7,38 @@ root,/apps/
 tempDir,${workDir}/${tmpName}/tmp/
 permanentDir,${workDir}/prm10
 toolchain,foss-2018b
+GCCcoreVersion,GCCcore-11.3.0
+
+##### Tools and versions #####
+jdkVersion,Java/11-LTS
+ngsUtilsVersion,ngs-utils/19.03.3-${GCCcoreVersion}
+ngsRNAVersion,NGS_RNA/beta
+fastqcVersion,FastQC/0.11.8-Java-11-LTS
+samtoolsVersion,SAMtools/1.9-${GCCcoreVersion}
+bedToolsVersion,BEDTools/2.28.0-${GCCcoreVersion}
+sambambaVersion,sambamba/0.7.0
+rVersion,R/3.6.1-${toolchain}-bare
+rPlusVersion,RPlus/3.6.1-${toolchain}-v21.10.1
+picardVersion,picard/2.20.5-Java-11-LTS
+htseqVersion,HTSeq/0.11.0-${GCCcoreVersion}-Python-3.7.4
+hisatVersion,hisat2/2.1.0-${toolchain}
+htsLibVersion,HTSlib/1.11-${GCCcoreVersion}
+pythonVersion,Python/3.7.4-${GCCcoreVersion}-bare
+python2Version,Python/2.7.16-${GCCcoreVersion}-bare
+python2PlusVersion,PythonPlus/2.7.16-${toolchain}-v20.12.1
+pythonPlusVersion,PythonPlus/3.7.4-${toolchain}-v20.02.1
+gatkVersion,GATK/4.1.4.1-Java-8-LTS
+multiqcVersion,multiqc_v1.12.sif
+starVersion,STAR/2.7.3a-${toolchain}
+picardJar,picard.jar
+gatkJar,gatk-package-4.1.4.1-local.jar
+mergeSamFilesJar,MergeSamFiles
+trimGaloreVersion,TrimGalore/0.4.5-${GCCcoreVersion}-Python-3.7.4-bare
+cutadaptVersion,cutadapt/2.6-${GCCcoreVersion}-Python-3.7.4-bare
+rSeQCVersion,RSeQC/3.0.1-${GCCcoreVersion}-Python-3.7.4
+leafcutterVersion,leafcutter/aa12b1e-${toolchain}
+vipVersion,vip/v3.3.1-${toolchain}
+outriderVersion,outrider_latest.sif
+rMATsVersion,rmats_v4.1.2.sif
+sifDir,/apps/data/GAD/singularity/
+rnaseqcVersion,${sifDir}/rnaseqc_2.4.2.sif
diff --git a/parameters.gearshift.csv b/parameters.gearshift.csv
index abf8467..a39eb5e 100755
--- a/parameters.gearshift.csv
+++ b/parameters.gearshift.csv
@@ -7,7 +7,7 @@ root,/apps/
 tempDir,${workDir}/${tmpName}/tmp/
 permanentDir,${workDir}/prm03
 toolchain,foss-2018b
-GCCcoreVersion,GCCcore-7.3.0
+GCCcoreVersion,GCCcore-11.3.0
 
 ##### Tools and versions #####
 jdkVersion,Java/11-LTS
diff --git a/parameters.talos.csv b/parameters.talos.csv
index 3600453..2014da4 100755
--- a/parameters.talos.csv
+++ b/parameters.talos.csv
@@ -8,3 +8,37 @@ tempDir,${workDir}/${tmpName}/tmp/
 permanentDir,${workDir}/prm08
 toolchain,foss-2022a
 GCCcoreVersion,GCCcore-11.3.0
+
+##### Tools and versions #####
+jdkVersion,Java/11-LTS
+ngsUtilsVersion,ngs-utils/19.03.3-${GCCcoreVersion}
+ngsRNAVersion,NGS_RNA/beta
+fastqcVersion,FastQC/0.11.8-Java-11-LTS
+samtoolsVersion,SAMtools/1.9-${GCCcoreVersion}
+bedToolsVersion,BEDTools/2.28.0-${GCCcoreVersion}
+sambambaVersion,sambamba/0.7.0
+rVersion,R/3.6.1-${toolchain}-bare
+rPlusVersion,RPlus/3.6.1-${toolchain}-v21.10.1
+picardVersion,picard/2.20.5-Java-11-LTS
+htseqVersion,HTSeq/0.11.0-${GCCcoreVersion}-Python-3.7.4
+hisatVersion,hisat2/2.1.0-${toolchain}
+htsLibVersion,HTSlib/1.11-${GCCcoreVersion}
+pythonVersion,Python/3.7.4-${GCCcoreVersion}-bare
+python2Version,Python/2.7.16-${GCCcoreVersion}-bare
+python2PlusVersion,PythonPlus/2.7.16-${toolchain}-v20.12.1
+pythonPlusVersion,PythonPlus/3.7.4-${toolchain}-v20.02.1
+gatkVersion,GATK/4.1.4.1-Java-8-LTS
+multiqcVersion,multiqc_v1.12.sif
+starVersion,STAR/2.7.3a-${toolchain}
+picardJar,picard.jar
+gatkJar,gatk-package-4.1.4.1-local.jar
+mergeSamFilesJar,MergeSamFiles
+trimGaloreVersion,TrimGalore/0.4.5-${GCCcoreVersion}-Python-3.7.4-bare
+cutadaptVersion,cutadapt/2.6-${GCCcoreVersion}-Python-3.7.4-bare
+rSeQCVersion,RSeQC/3.0.1-${GCCcoreVersion}-Python-3.7.4
+leafcutterVersion,leafcutter/aa12b1e-${toolchain}
+vipVersion,vip/v3.3.1-${toolchain}
+outriderVersion,outrider_latest.sif
+rMATsVersion,rmats_v4.1.2.sif
+sifDir,/apps/data/GAD/singularity/
+rnaseqcVersion,${sifDir}/rnaseqc_2.4.2.sif

From adf16e56d51b58f4f3271e867b30a2c2fc48ca3b Mon Sep 17 00:00:00 2001
From: gerbenvandervries <gerbenvandervries@gmail.com>
Date: Thu, 2 Feb 2023 08:48:58 +0000
Subject: [PATCH 23/42] version update

---
 parameters.fender.csv       | 2 +-
 parameters.gearshift.csv    | 2 +-
 parameters.hyperchicken.csv | 2 +-
 parameters.talos.csv        | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/parameters.fender.csv b/parameters.fender.csv
index 5c32e60..a284f54 100755
--- a/parameters.fender.csv
+++ b/parameters.fender.csv
@@ -11,7 +11,7 @@ GCCcoreVersion,GCCcore-11.3.0
 
 ##### Tools and versions #####
 jdkVersion,Java/11-LTS
-ngsUtilsVersion,ngs-utils/19.03.3-${GCCcoreVersion}
+ngsUtilsVersion,ngs-utils/22.10.1
 ngsRNAVersion,NGS_RNA/beta
 fastqcVersion,FastQC/0.11.8-Java-11-LTS
 samtoolsVersion,SAMtools/1.9-${GCCcoreVersion}
diff --git a/parameters.gearshift.csv b/parameters.gearshift.csv
index a39eb5e..388a220 100755
--- a/parameters.gearshift.csv
+++ b/parameters.gearshift.csv
@@ -11,7 +11,7 @@ GCCcoreVersion,GCCcore-11.3.0
 
 ##### Tools and versions #####
 jdkVersion,Java/11-LTS
-ngsUtilsVersion,ngs-utils/19.03.3-${GCCcoreVersion}
+ngsUtilsVersion,ngs-utils/22.10.1
 ngsRNAVersion,NGS_RNA/beta
 fastqcVersion,FastQC/0.11.8-Java-11-LTS
 samtoolsVersion,SAMtools/1.9-${GCCcoreVersion}
diff --git a/parameters.hyperchicken.csv b/parameters.hyperchicken.csv
index 9e47809..5987a2c 100755
--- a/parameters.hyperchicken.csv
+++ b/parameters.hyperchicken.csv
@@ -11,7 +11,7 @@ GCCcoreVersion,GCCcore-11.3.0
 
 ##### Tools and versions #####
 jdkVersion,Java/11-LTS
-ngsUtilsVersion,ngs-utils/19.03.3-${GCCcoreVersion}
+ngsUtilsVersion,ngs-utils/22.10.1
 ngsRNAVersion,NGS_RNA/beta
 fastqcVersion,FastQC/0.11.8-Java-11-LTS
 samtoolsVersion,SAMtools/1.16.1-${GCCcoreVersion}
diff --git a/parameters.talos.csv b/parameters.talos.csv
index 2014da4..e581302 100755
--- a/parameters.talos.csv
+++ b/parameters.talos.csv
@@ -11,7 +11,7 @@ GCCcoreVersion,GCCcore-11.3.0
 
 ##### Tools and versions #####
 jdkVersion,Java/11-LTS
-ngsUtilsVersion,ngs-utils/19.03.3-${GCCcoreVersion}
+ngsUtilsVersion,ngs-utils/22.10.1
 ngsRNAVersion,NGS_RNA/beta
 fastqcVersion,FastQC/0.11.8-Java-11-LTS
 samtoolsVersion,SAMtools/1.9-${GCCcoreVersion}

From 4ea51890f3e4412dfdba2b4beaef4d03b30dc897 Mon Sep 17 00:00:00 2001
From: gerbenvandervries <gerbenvandervries@gmail.com>
Date: Thu, 2 Feb 2023 09:03:36 +0000
Subject: [PATCH 24/42] remove deprecated script

---
 protocols/CreateExternSamplesProjects.sh | 6 +-----
 protocols/CreateInhouseRnaSeqProjects.sh | 7 +------
 2 files changed, 2 insertions(+), 11 deletions(-)

diff --git a/protocols/CreateExternSamplesProjects.sh b/protocols/CreateExternSamplesProjects.sh
index c4644da..a7a09b3 100755
--- a/protocols/CreateExternSamplesProjects.sh
+++ b/protocols/CreateExternSamplesProjects.sh
@@ -90,11 +90,7 @@ cd "${ROCKETPOINT}" || exit
 
 module load "${ngsVersion}"
 
-#
-# Create subset of samples for this project.
-#
-
-extract_samples_from_GAF_list.pl --i "${worksheet}" --o "${projectJobsDir}/${project}.csv" --c project --q "${project}"
+cp "${worksheet}" "${projectJobsDir}/${project}.csv"
 
 #
 # Execute MOLGENIS/compute to create job scripts to analyse this project.
diff --git a/protocols/CreateInhouseRnaSeqProjects.sh b/protocols/CreateInhouseRnaSeqProjects.sh
index e3ee4c7..6734323 100755
--- a/protocols/CreateInhouseRnaSeqProjects.sh
+++ b/protocols/CreateInhouseRnaSeqProjects.sh
@@ -94,12 +94,7 @@ done
 cd "${ROCKETPOINT}" || exit
 
 
-#
-# Create subset of samples for this project.
-#
-
-
-extract_samples_from_GAF_list.pl --i "${worksheet}" --o "${projectJobsDir}/${project}.csv" --c project --q "${project}"
+cp "${worksheet}" "${projectJobsDir}/${project}.csv"
 
 #
 # Execute MOLGENIS/compute to create job scripts to analyse this project.

From e8e3b8b5b4fe7dcb1958b11c40247787d1fbcaca Mon Sep 17 00:00:00 2001
From: "Gerben van der Vries\" gerbenvandervries@gmail.com"
 <gerbenvandervries@github.com>
Date: Fri, 17 Feb 2023 08:20:59 +0000
Subject: [PATCH 25/42] .

---
 parameters.hyperchicken.csv | 2 +-
 test/test_pipeline.sh       | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/parameters.hyperchicken.csv b/parameters.hyperchicken.csv
index 5987a2c..60db264 100755
--- a/parameters.hyperchicken.csv
+++ b/parameters.hyperchicken.csv
@@ -2,7 +2,7 @@
 queue,atd
 workDir,/groups/${groupname}/
 dataDir,${root}/data/
-tmpName,tmp01
+tmpName,tmp09
 root,/apps/
 tempDir,${workDir}/${tmpName}/tmp/
 permanentDir,${workDir}/prm03
diff --git a/test/test_pipeline.sh b/test/test_pipeline.sh
index 982e9c2..8838d2a 100644
--- a/test/test_pipeline.sh
+++ b/test/test_pipeline.sh
@@ -81,7 +81,7 @@ function checkIfFinished(){
 	echo "${_projectName} test succeeded!"
 	echo ""
 }
-tmpdirectory="tmp01"
+tmpdirectory="tmp09"
 groupName="umcg-atd"
 NGS_RNA_VERSION="NGS_DNA/betaAutotest"
 
@@ -119,7 +119,7 @@ tail -1 workflow_STAR.csv | perl -p -e 's|,|\t|g' | awk '{print "s15_Autotest,te
 perl -pi -e 's|s09_OUTRIDER|#s09_OUTRIDER|g' test_workflow_STAR.csv
 perl -pi -e 's|s12_VIP|#s12_VIP|g' test_workflow_STAR.csv
 
-cp "${pipelinefolder}/test/results/"* "/groups/umcg-atd/tmp01/tmp/NGS_RNA/testdata_true/"
+cp "${pipelinefolder}/test/results/"* "${workfolder}/tmp/NGS_RNA/testdata_true/"
 
 preparePipeline
 

From ac6079aa921b66aeecac72408952a8468a149c52 Mon Sep 17 00:00:00 2001
From: gerbenvandervries <gerbenvandervries@gmail.com>
Date: Fri, 17 Feb 2023 08:48:15 +0000
Subject: [PATCH 26/42] trimgalore version

---
 parameters.hyperchicken.csv | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/parameters.hyperchicken.csv b/parameters.hyperchicken.csv
index 60db264..37845c8 100755
--- a/parameters.hyperchicken.csv
+++ b/parameters.hyperchicken.csv
@@ -33,7 +33,7 @@ starVersion,STAR/2.7.3a-${toolchain}
 picardJar,picard.jar
 gatkJar,gatk-package-4.1.4.1-local.jar
 mergeSamFilesJar,MergeSamFiles
-trimGaloreVersion,TrimGalore/0.4.5-${GCCcoreVersion}-Python-3.10.4-bare
+trimGaloreVersion,TrimGalore/0.6.7-${GCCcoreVersion}
 cutadaptVersion,cutadapt/4.2-${GCCcoreVersion}-Python-3.10.4-bare
 rSeQCVersion,RSeQC/3.0.1-${GCCcoreVersion}-Python-3.10.4
 leafcutterVersion,leafcutter/aa12b1e-${toolchain}

From ca212c90a85836b8fd07fa63496f07cbd1bca771 Mon Sep 17 00:00:00 2001
From: gerbenvandervries <gerbenvandervries@gmail.com>
Date: Fri, 17 Feb 2023 09:10:41 +0000
Subject: [PATCH 27/42] STAR version

---
 parameters.hyperchicken.csv | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/parameters.hyperchicken.csv b/parameters.hyperchicken.csv
index 37845c8..b97ecc7 100755
--- a/parameters.hyperchicken.csv
+++ b/parameters.hyperchicken.csv
@@ -29,7 +29,7 @@ python2PlusVersion,PythonPlus/2.7.16-${toolchain}-v20.12.1
 pythonPlusVersion,PythonPlus/3.10.4-${toolchain}-v22.11.3
 gatkVersion,GATK/4.1.4.1-Java-8-LTS
 multiqcVersion,multiqc_v1.12.sif
-starVersion,STAR/2.7.3a-${toolchain}
+starVersion,STAR/STAR/2.7.9a-${toolchain}
 picardJar,picard.jar
 gatkJar,gatk-package-4.1.4.1-local.jar
 mergeSamFilesJar,MergeSamFiles

From 68dcfec129b102f655acb155ff26660bc1844ace Mon Sep 17 00:00:00 2001
From: "Gerben van der Vries\" gerbenvandervries@gmail.com"
 <gerbenvandervries@gmail.com>
Date: Fri, 17 Feb 2023 09:15:45 +0000
Subject: [PATCH 28/42] .

---
 parameters.hyperchicken.csv | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/parameters.hyperchicken.csv b/parameters.hyperchicken.csv
index b97ecc7..42900f0 100755
--- a/parameters.hyperchicken.csv
+++ b/parameters.hyperchicken.csv
@@ -29,7 +29,7 @@ python2PlusVersion,PythonPlus/2.7.16-${toolchain}-v20.12.1
 pythonPlusVersion,PythonPlus/3.10.4-${toolchain}-v22.11.3
 gatkVersion,GATK/4.1.4.1-Java-8-LTS
 multiqcVersion,multiqc_v1.12.sif
-starVersion,STAR/STAR/2.7.9a-${toolchain}
+starVersion,STAR/2.7.9a-${GCCcoreVersion}
 picardJar,picard.jar
 gatkJar,gatk-package-4.1.4.1-local.jar
 mergeSamFilesJar,MergeSamFiles

From 3c1088aa2c1a63c3df873a6762c58719915860c0 Mon Sep 17 00:00:00 2001
From: "Gerben van der Vries\" gerbenvandervries@gmail.com"
 <gerbenvandervries@gmail.com>
Date: Wed, 1 Mar 2023 14:48:11 +0000
Subject: [PATCH 29/42] STAR ref change

---
 parameters.homo_sapiens.GRCh37.csv | 2 +-
 parameters.hyperchicken.csv        | 3 ++-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/parameters.homo_sapiens.GRCh37.csv b/parameters.homo_sapiens.GRCh37.csv
index 07ad53b..b6ac19d 100755
--- a/parameters.homo_sapiens.GRCh37.csv
+++ b/parameters.homo_sapiens.GRCh37.csv
@@ -130,7 +130,7 @@ gtexJunc,/apps/data/GAD/others/GTEx_v7_bflb_junctions.gct
 omimList,/apps/data/GAD/others/OMIM2.list
 indexFile,${indexSpecies}
 dbsnpVcf,/apps/data/dbSNP/dbsnp_137.b37.vcf
-starIndex,/apps/data/Ensembl/GrCh37.75/pub/release-75/fasta/homo_sapiens/STAR-2.7.3a-${GCCcoreVersion}/
+starIndex,/apps/data/Ensembl/GrCh37.75/pub/release-75/fasta/homo_sapiens/STAR-2.7.9a-${GCCVersion}/
 #### GENOME VARIABLES ####
 genome,GRCh37
 ensembleReleaseVersion,75
diff --git a/parameters.hyperchicken.csv b/parameters.hyperchicken.csv
index 42900f0..6d1d6f8 100755
--- a/parameters.hyperchicken.csv
+++ b/parameters.hyperchicken.csv
@@ -8,6 +8,7 @@ tempDir,${workDir}/${tmpName}/tmp/
 permanentDir,${workDir}/prm03
 toolchain,foss-2022a
 GCCcoreVersion,GCCcore-11.3.0
+GCCVersion,GCC-11.3.0
 
 ##### Tools and versions #####
 jdkVersion,Java/11-LTS
@@ -29,7 +30,7 @@ python2PlusVersion,PythonPlus/2.7.16-${toolchain}-v20.12.1
 pythonPlusVersion,PythonPlus/3.10.4-${toolchain}-v22.11.3
 gatkVersion,GATK/4.1.4.1-Java-8-LTS
 multiqcVersion,multiqc_v1.12.sif
-starVersion,STAR/2.7.9a-${GCCcoreVersion}
+starVersion,STAR/2.7.9a-GCC-11.3.0
 picardJar,picard.jar
 gatkJar,gatk-package-4.1.4.1-local.jar
 mergeSamFilesJar,MergeSamFiles

From 797d5f935bc4702a1180dd6c074600fbbc2aabc5 Mon Sep 17 00:00:00 2001
From: "Gerben van der Vries\" gerbenvandervries@gmail.com"
 <gerbenvandervries@gmail.com>
Date: Thu, 2 Mar 2023 09:48:58 +0000
Subject: [PATCH 30/42] version

---
 parameters.homo_sapiens.GRCh37.csv | 2 +-
 parameters.hyperchicken.csv        | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/parameters.homo_sapiens.GRCh37.csv b/parameters.homo_sapiens.GRCh37.csv
index b6ac19d..c86ac6c 100755
--- a/parameters.homo_sapiens.GRCh37.csv
+++ b/parameters.homo_sapiens.GRCh37.csv
@@ -130,7 +130,7 @@ gtexJunc,/apps/data/GAD/others/GTEx_v7_bflb_junctions.gct
 omimList,/apps/data/GAD/others/OMIM2.list
 indexFile,${indexSpecies}
 dbsnpVcf,/apps/data/dbSNP/dbsnp_137.b37.vcf
-starIndex,/apps/data/Ensembl/GrCh37.75/pub/release-75/fasta/homo_sapiens/STAR-2.7.9a-${GCCVersion}/
+starIndex,/apps/data/Ensembl/GrCh37.75/pub/release-75/fasta/homo_sapiens/STAR-2.7.3a-foss-2018b/
 #### GENOME VARIABLES ####
 genome,GRCh37
 ensembleReleaseVersion,75
diff --git a/parameters.hyperchicken.csv b/parameters.hyperchicken.csv
index 6d1d6f8..8c56e0a 100755
--- a/parameters.hyperchicken.csv
+++ b/parameters.hyperchicken.csv
@@ -30,7 +30,7 @@ python2PlusVersion,PythonPlus/2.7.16-${toolchain}-v20.12.1
 pythonPlusVersion,PythonPlus/3.10.4-${toolchain}-v22.11.3
 gatkVersion,GATK/4.1.4.1-Java-8-LTS
 multiqcVersion,multiqc_v1.12.sif
-starVersion,STAR/2.7.9a-GCC-11.3.0
+starVersion,2.7.3a-GCC-11.3.0
 picardJar,picard.jar
 gatkJar,gatk-package-4.1.4.1-local.jar
 mergeSamFilesJar,MergeSamFiles

From e7e18fe39bf72138694820364222fd1caf63e75c Mon Sep 17 00:00:00 2001
From: "Gerben van der Vries\" gerbenvandervries@gmail.com"
 <gerbenvandervries@gmail.com>
Date: Thu, 2 Mar 2023 10:28:51 +0000
Subject: [PATCH 31/42] version fix, and bugfix strandedness

---
 parameters.hyperchicken.csv | 2 +-
 protocols/QCStats.sh        | 2 +-
 protocols/rMATs.sh          | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/parameters.hyperchicken.csv b/parameters.hyperchicken.csv
index 8c56e0a..22fefbe 100755
--- a/parameters.hyperchicken.csv
+++ b/parameters.hyperchicken.csv
@@ -30,7 +30,7 @@ python2PlusVersion,PythonPlus/2.7.16-${toolchain}-v20.12.1
 pythonPlusVersion,PythonPlus/3.10.4-${toolchain}-v22.11.3
 gatkVersion,GATK/4.1.4.1-Java-8-LTS
 multiqcVersion,multiqc_v1.12.sif
-starVersion,2.7.3a-GCC-11.3.0
+starVersion,STAR/2.7.3a-GCC-11.3.0
 picardJar,picard.jar
 gatkJar,gatk-package-4.1.4.1-local.jar
 mergeSamFilesJar,MergeSamFiles
diff --git a/protocols/QCStats.sh b/protocols/QCStats.sh
index 14f64b1..a9833dd 100755
--- a/protocols/QCStats.sh
+++ b/protocols/QCStats.sh
@@ -44,7 +44,7 @@ module list
 num1="$(tail -n 2 "${strandedness}" | awk '{print $7}' | head -n 1)"
 num2="$(tail -n 1 "${strandedness}" | awk '{print $7}')"
 
-STRANDED=$(echo -e "${num1}\t${num2}" | awk '{if ($1 > 0.6){print "SECOND_READ_TRANSCRIPTION_STRAND"}else if($2 > 0.6){print "FIRST_READ_TRANSCRIPTION_STRAND"}else if($1 < 0.6 && $2 < 0.6){print "NONE"} }')
+STRANDED=$(echo -e "${num1}\t${num2}" | awk '{if ($1 > 0.6){print "FIRST_READ_TRANSCRIPTION_STRAND"}else if($2 > 0.6){print "SECOND_READ_TRANSCRIPTION_STRAND"}else if($1 < 0.6 && $2 < 0.6){print "NONE"} }')
 
 #If paired-end do fastqc for both ends, else only for one
 if [[ "${seqType}" == "PE" ]]
diff --git a/protocols/rMATs.sh b/protocols/rMATs.sh
index 0d723b6..ceffd13 100755
--- a/protocols/rMATs.sh
+++ b/protocols/rMATs.sh
@@ -48,7 +48,7 @@ done < "${intermediateDir}${externalSampleID}.SJ.design.tsv"
 num1="$(tail -n 2 "${strandedness}" | awk '{print $7}' | head -n 1)"
 num2="$(tail -n 1 "${strandedness}" | awk '{print $7}')"
 
-STRANDED=$(echo -e "${num1}\t${num2}" | awk '{if ($1 > 0.6){print "fr-secondstrand"}else if($2 > 0.6){print "fr-firststrand"}else if($1 < 0.6 && $2 < 0.6){print "fr-unstranded"} }')
+STRANDED=$(echo -e "${num1}\t${num2}" | awk '{if ($1 > 0.6){print "fr-firststrand"}else if($2 > 0.6){print "fr-secondstrand"}else if($1 < 0.6 && $2 < 0.6){print "fr-unstranded"} }')
 
 singularity exec --bind "${intermediateDir}":/intermediateDir,/apps:/apps,/groups:/groups "${sifDir}/${rMATsVersion}" python /rmats/rmats.py \
 --b1 "/intermediateDir/${externalSampleID}.B1.txt" --b2 "/intermediateDir/${externalSampleID}.B2.txt" \

From 2bad75547d346f831a29a3bf2e85ce17bc32cd16 Mon Sep 17 00:00:00 2001
From: "Gerben van der Vries\" gerbenvandervries@gmail.com"
 <gerbenvandervries@gmail.com>
Date: Thu, 2 Mar 2023 15:03:03 +0000
Subject: [PATCH 32/42] versions

---
 parameters.hyperchicken.csv | 2 +-
 protocols/Design.sh         | 5 +----
 2 files changed, 2 insertions(+), 5 deletions(-)

diff --git a/parameters.hyperchicken.csv b/parameters.hyperchicken.csv
index 22fefbe..d4de494 100755
--- a/parameters.hyperchicken.csv
+++ b/parameters.hyperchicken.csv
@@ -28,7 +28,7 @@ pythonVersion,Python/3.10.4-${GCCcoreVersion}-bare
 python2Version,Python/2.7.16-${GCCcoreVersion}-bare
 python2PlusVersion,PythonPlus/2.7.16-${toolchain}-v20.12.1
 pythonPlusVersion,PythonPlus/3.10.4-${toolchain}-v22.11.3
-gatkVersion,GATK/4.1.4.1-Java-8-LTS
+gatkVersion,GATK/4.2.4.1-Java-8-LTS
 multiqcVersion,multiqc_v1.12.sif
 starVersion,STAR/2.7.3a-GCC-11.3.0
 picardJar,picard.jar
diff --git a/protocols/Design.sh b/protocols/Design.sh
index 041e16f..3255706 100755
--- a/protocols/Design.sh
+++ b/protocols/Design.sh
@@ -1,5 +1,5 @@
 set -o pipefail
-#MOLGENIS nodes=1 ppn=4 mem=4gb walltime=05:59:00
+#MOLGENIS nodes=1 ppn=1 mem=4gb walltime=05:59:00
 
 #Parameter mapping
 #string rPlusVersion
@@ -10,9 +10,6 @@ set -o pipefail
 #string tmpName
 #string logsDir
 
-module load "${rPlusVersion}"
-module list
-
 #Function to check if array contains value
 array_contains () {
 	local array="$1[@]"

From b25ca38499c45ec9a2c73334e812eb43a2053c9c Mon Sep 17 00:00:00 2001
From: "Gerben van der Vries\" gerbenvandervries@gmail.com"
 <gerbenvandervries@gmail.com>
Date: Thu, 9 Mar 2023 12:47:09 +0000
Subject: [PATCH 33/42] leafcutter

---
 parameters.hyperchicken.csv | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/parameters.hyperchicken.csv b/parameters.hyperchicken.csv
index d4de494..f4046fa 100755
--- a/parameters.hyperchicken.csv
+++ b/parameters.hyperchicken.csv
@@ -19,7 +19,7 @@ samtoolsVersion,SAMtools/1.16.1-${GCCcoreVersion}
 bedToolsVersion,BEDTools/2.30.0-${GCCcoreVersion}
 sambambaVersion,sambamba/0.7.0
 rVersion,R/4.2.1-${toolchain}-bare
-rPlusVersion,RPlus/4.2.1-${toolchain}-v21.10.1
+rPlusVersion,RPlus/4.2.1-${toolchain}-v23.01.1
 picardVersion,picard/2.26.10-Java-8-LTS
 htseqVersion,HTSeq/0.11.0-${GCCcoreVersion}-Python-3.10.4
 hisatVersion,hisat2/2.1.0-${toolchain}
@@ -37,7 +37,7 @@ mergeSamFilesJar,MergeSamFiles
 trimGaloreVersion,TrimGalore/0.6.7-${GCCcoreVersion}
 cutadaptVersion,cutadapt/4.2-${GCCcoreVersion}-Python-3.10.4-bare
 rSeQCVersion,RSeQC/3.0.1-${GCCcoreVersion}-Python-3.10.4
-leafcutterVersion,leafcutter/aa12b1e-${toolchain}
+leafcutterVersion,leafcutter/aa12b1e-${GCCcoreVersion}
 vipVersion,vip/v3.3.1-${toolchain}
 outriderVersion,outrider_latest.sif
 rMATsVersion,rmats_v4.1.2.sif

From e5b7dc56f6a18afafaae639dfe06fd55597bf0f7 Mon Sep 17 00:00:00 2001
From: "Gerben van der Vries\" gerbenvandervries@gmail.com"
 <gerbenvandervries@gmail.com>
Date: Fri, 10 Mar 2023 15:12:23 +0000
Subject: [PATCH 34/42] fixes

---
 parameters.hyperchicken.csv               |  2 +-
 protocols/BQSR.sh                         |  4 ++--
 protocols/Leafcutter.sh                   |  2 ++
 protocols/Leafcutter_intron_clustering.sh |  4 ++--
 protocols/Leafcutter_rare.sh              | 10 ++--------
 protocols/SplitAndTrim.sh                 |  2 +-
 6 files changed, 10 insertions(+), 14 deletions(-)

diff --git a/parameters.hyperchicken.csv b/parameters.hyperchicken.csv
index f4046fa..dde8459 100755
--- a/parameters.hyperchicken.csv
+++ b/parameters.hyperchicken.csv
@@ -26,7 +26,7 @@ hisatVersion,hisat2/2.1.0-${toolchain}
 htsLibVersion,HTSlib/1.16-${GCCcoreVersion}
 pythonVersion,Python/3.10.4-${GCCcoreVersion}-bare
 python2Version,Python/2.7.16-${GCCcoreVersion}-bare
-python2PlusVersion,PythonPlus/2.7.16-${toolchain}-v20.12.1
+python2PlusVersion,PythonPlus/2.7.16-foss-2018b-v21.08.1
 pythonPlusVersion,PythonPlus/3.10.4-${toolchain}-v22.11.3
 gatkVersion,GATK/4.2.4.1-Java-8-LTS
 multiqcVersion,multiqc_v1.12.sif
diff --git a/protocols/BQSR.sh b/protocols/BQSR.sh
index 4c1cbce..4c4a763 100755
--- a/protocols/BQSR.sh
+++ b/protocols/BQSR.sh
@@ -37,14 +37,14 @@ echo "Running GATK BQSR:"
 
 
 java -jar -Xmx7g -XX:ParallelGCThreads=2 -Djava.io.tmpdir="${tmpTmpDataDir}" \
-"${EBROOTGATK}/gatk-package-4.1.4.1-local.jar" BaseRecalibrator \
+"${EBROOTGATK}/gatk-package-4.2.4.1-local.jar" BaseRecalibrator \
 -R "${indexFile}" \
 -I "${splitAndTrimBam}" \
 -O "${bqsrBeforeGrp}" \
 --known-sites "${dbsnpVcf}"
 
 java -jar -Xmx7g -XX:ParallelGCThreads=2 -Djava.io.tmpdir="${tmpTmpDataDir}" \
-"${EBROOTGATK}/gatk-package-4.1.4.1-local.jar" ApplyBQSR \
+"${EBROOTGATK}/gatk-package-4.2.4.1-local.jar" ApplyBQSR \
 -R "${indexFile}" \
 -I "${splitAndTrimBam}" \
 -O "${tmpBqsrBam}" \
diff --git a/protocols/Leafcutter.sh b/protocols/Leafcutter.sh
index f94158f..21c08d3 100755
--- a/protocols/Leafcutter.sh
+++ b/protocols/Leafcutter.sh
@@ -47,6 +47,8 @@ awk -F',' -v id="${colID[0]}" -v con="${colArray[0]}" '{print $id".sorted.merged
 sed 1d "${intermediateDir}${project}_groups_file.txt" > "${intermediateDir}${project}"_groups_file.txt.tmp
 mv "${intermediateDir}${project}_groups_file.txt.tmp" "${intermediateDir}${project}_groups_file.txt"
 
+export R_LIBS_USER="${EBROOTLEAFCUTTER}/R_LIBS/"
+
 echo "conditionCount = ${conditionCount}"
 if [[ "${conditionCount}" -gt 1 ]]
 then
diff --git a/protocols/Leafcutter_intron_clustering.sh b/protocols/Leafcutter_intron_clustering.sh
index 4505c8e..8c3944b 100755
--- a/protocols/Leafcutter_intron_clustering.sh
+++ b/protocols/Leafcutter_intron_clustering.sh
@@ -20,7 +20,7 @@ module list
 num1="$(tail -n 2 "${strandedness}" | awk '{print $7}' | head -n 1)"
 num2="$(tail -n 1 "${strandedness}" | awk '{print $7}')"
 
-STRANDED=$(echo -e "${num1}\t${num2}" | awk '{if ($1 > 0.6){print "1"}else if($2 > 0.6){print "2"}else if($1 < 0.6 && $2 < 0.6){print "0"} }')
+STRANDED=$(echo -e "${num1}\t${num2}" | awk '{if ($1 > 0.6){print "RF"}else if($2 > 0.6){print "FR"}else if($1 < 0.6 && $2 < 0.6){print "XS"} }')
 
 echo -e "\nWith strandedness type: ${STRANDED},
 where (0 = unstranded, 1 = first-strand/RF, 2, = second-strand/FR)."
@@ -38,7 +38,7 @@ do
 	-a 8 \
 	-m 50 \
 	-M 500000 \
-	-s 0 \
+	-s "${STRANDED}" \
 	"${bamfile}" \
 	-o "${bamfile}.junc"
 
diff --git a/protocols/Leafcutter_rare.sh b/protocols/Leafcutter_rare.sh
index 4288da1..08dabdc 100755
--- a/protocols/Leafcutter_rare.sh
+++ b/protocols/Leafcutter_rare.sh
@@ -23,6 +23,8 @@ module load "${leafcutterVersion}"
 module load "${python2Version}"
 module list
 
+export R_LIBS_USER="${EBROOTLEAFCUTTER}/R_LIBS/"
+
 	"${EBROOTLEAFCUTTER}/scripts/leafcutter_ds.R" \
 	-e "${annotationTxt}" \
 	--num_threads 4 \
@@ -33,12 +35,4 @@ module list
 	"${intermediateDir}/${project}_leafcutter_cluster_regtools_perind_numers.counts.gz" \
 	"${intermediateDir}/${externalSampleID}.SJ.design.tsv"
 
-	Rscript "${EBROOTLEAFCUTTER}/scripts/ds_plots.R" \
-	-e "${gencodeHg19AllExons}" \
-	-o "${tmpintermediateDir}/${externalSampleID}_leafcutter_ds" \
-	"${intermediateDir}/${project}_leafcutter_cluster_regtools_perind_numers.counts.gz" \
-	"${intermediateDir}/${externalSampleID}.SJ.design.tsv" \
-	"${tmpintermediateDir}/${externalSampleID}.leafcutter.outlier_cluster_significance.txt" \
-	-f 0.05
-
 	mv "${tmpintermediateDir}/${externalSampleID}"* "${intermediateDir}"
diff --git a/protocols/SplitAndTrim.sh b/protocols/SplitAndTrim.sh
index ce9f759..73df6bd 100755
--- a/protocols/SplitAndTrim.sh
+++ b/protocols/SplitAndTrim.sh
@@ -38,7 +38,7 @@ module list
 
 java -Xmx10g -XX:ParallelGCThreads=2 \
 -Djava.io.tmpdir="${tmpTmpDataDir}" \
--jar "${EBROOTGATK}/gatk-package-4.1.4.1-local.jar" SplitNCigarReads \
+-jar "${EBROOTGATK}/gatk-package-4.2.4.1-local.jar" SplitNCigarReads \
 --tmp-dir "${tmpTmpDataDir}" \
 -R "${indexFile}" \
 -I "${sampleMergedDedupBam}" \

From 395ba654b17fe5d8b179fe7a9382d3a92052b38b Mon Sep 17 00:00:00 2001
From: "Gerben van der Vries\" gerbenvandervries@gmail.com"
 <gerbenvandervries@gmail.com>
Date: Tue, 14 Mar 2023 09:12:34 +0000
Subject: [PATCH 35/42] version

---
 parameters.hyperchicken.csv | 2 +-
 protocols/BQSR.sh           | 3 ++-
 protocols/SplitAndTrim.sh   | 2 +-
 3 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/parameters.hyperchicken.csv b/parameters.hyperchicken.csv
index dde8459..6152cf0 100755
--- a/parameters.hyperchicken.csv
+++ b/parameters.hyperchicken.csv
@@ -28,7 +28,7 @@ pythonVersion,Python/3.10.4-${GCCcoreVersion}-bare
 python2Version,Python/2.7.16-${GCCcoreVersion}-bare
 python2PlusVersion,PythonPlus/2.7.16-foss-2018b-v21.08.1
 pythonPlusVersion,PythonPlus/3.10.4-${toolchain}-v22.11.3
-gatkVersion,GATK/4.2.4.1-Java-8-LTS
+gatkVersion,GATK/4.1.4.1-Java-8-LTS
 multiqcVersion,multiqc_v1.12.sif
 starVersion,STAR/2.7.3a-GCC-11.3.0
 picardJar,picard.jar
diff --git a/protocols/BQSR.sh b/protocols/BQSR.sh
index 4c4a763..79c8823 100755
--- a/protocols/BQSR.sh
+++ b/protocols/BQSR.sh
@@ -5,6 +5,7 @@ set -o pipefail
 #string stage
 #string checkStage
 #string gatkVersion
+#string gatkJar
 #string intermediateDir
 #string	externalSampleID
 #string bqsrBam
@@ -37,7 +38,7 @@ echo "Running GATK BQSR:"
 
 
 java -jar -Xmx7g -XX:ParallelGCThreads=2 -Djava.io.tmpdir="${tmpTmpDataDir}" \
-"${EBROOTGATK}/gatk-package-4.2.4.1-local.jar" BaseRecalibrator \
+"${EBROOTGATK}/${gatkJar}" BaseRecalibrator \
 -R "${indexFile}" \
 -I "${splitAndTrimBam}" \
 -O "${bqsrBeforeGrp}" \
diff --git a/protocols/SplitAndTrim.sh b/protocols/SplitAndTrim.sh
index 73df6bd..aec4b20 100755
--- a/protocols/SplitAndTrim.sh
+++ b/protocols/SplitAndTrim.sh
@@ -38,7 +38,7 @@ module list
 
 java -Xmx10g -XX:ParallelGCThreads=2 \
 -Djava.io.tmpdir="${tmpTmpDataDir}" \
--jar "${EBROOTGATK}/gatk-package-4.2.4.1-local.jar" SplitNCigarReads \
+-jar "${EBROOTGATK}/${gatkJar}" SplitNCigarReads \
 --tmp-dir "${tmpTmpDataDir}" \
 -R "${indexFile}" \
 -I "${sampleMergedDedupBam}" \

From a54de8a82b7ee6e2d7c05547add9a0ff937ebb79 Mon Sep 17 00:00:00 2001
From: "Gerben van der Vries\" gerbenvandervries@gmail.com"
 <gerbenvandervries@gmail.com>
Date: Wed, 15 Mar 2023 12:22:20 +0000
Subject: [PATCH 36/42] trigger, atotest

---
 protocols/BQSR.sh          | 2 +-
 protocols/QCStats.sh       | 2 ++
 test/protocols/Autotest.sh | 2 +-
 3 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/protocols/BQSR.sh b/protocols/BQSR.sh
index 79c8823..19fc826 100755
--- a/protocols/BQSR.sh
+++ b/protocols/BQSR.sh
@@ -45,7 +45,7 @@ java -jar -Xmx7g -XX:ParallelGCThreads=2 -Djava.io.tmpdir="${tmpTmpDataDir}" \
 --known-sites "${dbsnpVcf}"
 
 java -jar -Xmx7g -XX:ParallelGCThreads=2 -Djava.io.tmpdir="${tmpTmpDataDir}" \
-"${EBROOTGATK}/gatk-package-4.2.4.1-local.jar" ApplyBQSR \
+"${EBROOTGATK}/${gatkJar}" ApplyBQSR \
 -R "${indexFile}" \
 -I "${splitAndTrimBam}" \
 -O "${tmpBqsrBam}" \
diff --git a/protocols/QCStats.sh b/protocols/QCStats.sh
index a9833dd..0aad218 100755
--- a/protocols/QCStats.sh
+++ b/protocols/QCStats.sh
@@ -25,6 +25,7 @@ set -o pipefail
 #string picardVersion
 #string samtoolsVersion
 #string ngsVersion
+#string rPlusVersion
 #string pythonVersion
 #string picardJar
 #string project
@@ -38,6 +39,7 @@ module load "${picardVersion}"
 module load "${samtoolsVersion}"
 module load "${pythonVersion}"
 module load "${ngsVersion}"
+module load "${rPlusVersion}"
 module list
 
 # Get strandness.
diff --git a/test/protocols/Autotest.sh b/test/protocols/Autotest.sh
index d112f82..02ad6c0 100755
--- a/test/protocols/Autotest.sh
+++ b/test/protocols/Autotest.sh
@@ -9,7 +9,7 @@
 #tmp fix
 export TERM='xterm'
 
-testResults="/groups/umcg-atd/tmp01/tmp/NGS_RNA/testdata_true/"
+testResults="/groups/umcg-atd/${tmpName}/tmp/NGS_RNA/testdata_true/"
 mkdir -p "${testResults}/output_NGS_RNA"
 
 module load ngs-utils

From d8340a7f0e06cde45798f397aacbedb17075c026 Mon Sep 17 00:00:00 2001
From: "Gerben van der Vries\" gerbenvandervries@gmail.com"
 <gerbenvandervries@gmail.com>
Date: Thu, 16 Mar 2023 09:45:40 +0000
Subject: [PATCH 37/42] trigger

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

diff --git a/README.md b/README.md
index 6744355..1f4e268 100644
--- a/README.md
+++ b/README.md
@@ -1,4 +1,4 @@
-<h1>NGS_RNA pipeline</h1>
+<h1>NGS_RNA pipeline</h1> 
 
 <h2>Description of the different steps used in the RNA analysis pipeline </h2>
 

From 1066d770444711783a1c1001046b8430ffd1d5d0 Mon Sep 17 00:00:00 2001
From: "Gerben van der Vries\" gerbenvandervries@gmail.com"
 <gerbenvandervries@gmail.com>
Date: Thu, 16 Mar 2023 10:18:54 +0000
Subject: [PATCH 38/42] update core, and testtime

---
 protocols/CombineFastq.sh         | 2 +-
 protocols/DE.sh                   | 2 +-
 protocols/MarkDuplicates.sh       | 2 +-
 protocols/TrimReads_TrimGalore.sh | 2 +-
 test/test_pipeline.sh             | 4 ++--
 5 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/protocols/CombineFastq.sh b/protocols/CombineFastq.sh
index 9fc3596..5df758b 100644
--- a/protocols/CombineFastq.sh
+++ b/protocols/CombineFastq.sh
@@ -1,5 +1,5 @@
 set -o pipefail
-#MOLGENIS walltime=23:59:00 mem=8gb ppn=6
+#MOLGENIS walltime=23:59:00 mem=8gb ppn=1
 
 #Parameter mapping
 #string tempDir
diff --git a/protocols/DE.sh b/protocols/DE.sh
index b30ac6a..669b89a 100755
--- a/protocols/DE.sh
+++ b/protocols/DE.sh
@@ -1,5 +1,5 @@
 set -o pipefail
-#MOLGENIS nodes=1 ppn=4 mem=4gb walltime=05:59:00
+#MOLGENIS nodes=1 ppn=1 mem=4gb walltime=05:59:00
 
 #Parameter mapping
 #string rPlusVersion
diff --git a/protocols/MarkDuplicates.sh b/protocols/MarkDuplicates.sh
index ec68e75..cdce494 100755
--- a/protocols/MarkDuplicates.sh
+++ b/protocols/MarkDuplicates.sh
@@ -1,6 +1,6 @@
 set -o pipefail
 #!/bin/bash
-#MOLGENIS walltime=23:59:00 mem=8gb ppn=6
+#MOLGENIS walltime=23:59:00 mem=8gb ppn=4
 
 #Parameter mapping
 #string picardVersion
diff --git a/protocols/TrimReads_TrimGalore.sh b/protocols/TrimReads_TrimGalore.sh
index 92c2e30..4715f60 100755
--- a/protocols/TrimReads_TrimGalore.sh
+++ b/protocols/TrimReads_TrimGalore.sh
@@ -1,5 +1,5 @@
 set -o pipefail
-#MOLGENIS nodes=1 ppn=4 mem=4gb walltime=23:59:00
+#MOLGENIS nodes=1 ppn=1 mem=4gb walltime=23:59:00
 
 #Parameter mapping
 #string seqType
diff --git a/test/test_pipeline.sh b/test/test_pipeline.sh
index 8838d2a..9428dad 100644
--- a/test/test_pipeline.sh
+++ b/test/test_pipeline.sh
@@ -63,9 +63,9 @@ function checkIfFinished(){
 		minutes=$((minutes+2))
 
 		count=$((count+2))
-		if [ $count -eq 30 ]
+		if [ $count -eq 35 ]
 		then
-			echo "the test was not finished within 30 minutes, let's kill it"
+			echo "the test was not finished within 35 minutes, let's kill it"
 			echo -e "\n"
 			for i in ${workfolder}/projects/${_projectName}/run01/jobs/*.sh
 			do

From 3d8f61eaa0b903b1a89f81bdbbb82e1af555a764 Mon Sep 17 00:00:00 2001
From: "Gerben van der Vries\" gerbenvandervries@gmail.com"
 <gerbenvandervries@gmail.com>
Date: Thu, 16 Mar 2023 11:35:49 +0000
Subject: [PATCH 39/42] .

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

diff --git a/README.md b/README.md
index 1f4e268..6744355 100644
--- a/README.md
+++ b/README.md
@@ -1,4 +1,4 @@
-<h1>NGS_RNA pipeline</h1> 
+<h1>NGS_RNA pipeline</h1>
 
 <h2>Description of the different steps used in the RNA analysis pipeline </h2>
 

From e6e5566b743de9b074ce725ec3dd0f657ffebb36 Mon Sep 17 00:00:00 2001
From: Pieter Neerincx <pieter.neerincx@gmail.com>
Date: Mon, 19 Jun 2023 21:49:35 +0200
Subject: [PATCH 40/42] Updated shellcheck test script: synced with updates
 previously already applied to other repos.

---
 check/shellcheck.sh | 49 +++++++++++++++------------------------------
 1 file changed, 16 insertions(+), 33 deletions(-)

diff --git a/check/shellcheck.sh b/check/shellcheck.sh
index 23bc1d9..7f02914 100755
--- a/check/shellcheck.sh
+++ b/check/shellcheck.sh
@@ -1,5 +1,9 @@
 #!/bin/bash
 
+set -e
+set -u
+set -o pipefail
+
 #
 # Disable some shellcheck warnings:
 #  * SC2004: $/${} is unnecessary on arithmetic variables.
@@ -7,12 +11,9 @@
 #  * SC2015: Note that A && B || C is not if-then-else. C may run when A is true.
 #            We know and use this construct regularly to create "transactions"
 #            where C is only executed when both A and B have succeeded.
-#  * SC2154: Due to Molgenis Compute string initialization the warning is not valid 
-#
-#  * SC2148: the shebang is declared in the header.ftl not in the protocols
+#  * SC2148: The shebang is declared in the header.ftl and not in the protocols.
 #
-
-export SHELLCHECK_OPTS="-e SC2004 -e SC2015 -e SC2154 -e SC2148"
+export SHELLCHECK_OPTS="-e SC2004 -e SC2015 -e SC2148"
 
 function showHelp() {
 	#
@@ -35,6 +36,7 @@ EOH
 #
 # Parse commandline options
 #
+declare format='gcc'  # default
 while getopts ":hv" opt
 do
 	case "${opt}" in
@@ -42,7 +44,7 @@ do
 			showHelp
 			;;
 		v)
-			verbose='1'
+			format='tty'
 			;;
 		\?)
 			printf '%s\n' "FATAL: Invalid option -${OPTARG}. Try $(basename "${0}") -h for help."
@@ -68,14 +70,13 @@ which shellcheck 2>&1 >/dev/null \
 		exit 1
 	}
 
+MYDIR="$(cd -P "$(dirname "${0}")" && pwd)"
 #
-# Run ShellCheck for all Bash scripts in the bin/ subdir.
-#  * Includes sourced files, so the libraries from the lib/ subfolder 
+# Run ShellCheck for all Bash scripts in the protocols/ subdir.
+#  * Includes sourced files, so files in a subfolder 
 #    are checked too as long a they are used in at least one script.
-#  * Select format and output based on whether this script is 
-#    executed by Jenkins or by a regular user.
 #
-if [[ -n "${WORKSPACE:-}" ]]
+if [[ "${CIRCLECI:-}" == true ]]
 then
 	#
 	# Exclude SC2154 (warning for variables that are referenced but not assigned),
@@ -83,27 +84,9 @@ then
 	#
 	export SHELLCHECK_OPTS="${SHELLCHECK_OPTS} -e SC2154"
 	#
-	# ShellCheck for Jenkins.
-	#
-	shellcheck -a -x -o all -f checkstyle "${WORKSPACE}"/protocols/*.sh | tee checkstyle-result.xml
-	#
-	# Reformat the generated report to add hyperlinks to the ShellCheck issues on the wiki:
-	#	https://github.com/koalaman/shellcheck/wiki/SC${ISSUENUMBER}
-	# explaining what is wrong with the code / style and how to improve it.
-	#
-	perl -pi -e "s|message='([^']+)'\s+source='ShellCheck.(SC[0-9]+)'|message='&lt;a href=&quot;https://github.com/koalaman/shellcheck/wiki/\$2&quot;&gt;\$2: 
-\$1&lt;/a&gt;' source='ShellCheck.\$2'|" checkstyle-result.xml
-else
-	#
-	# ShellCheck for regular user on the commandline.
+	# Exclude SC2312 (warning for masking return values of command in a subshell when using process substitution) temporarily,
+	# because we did not find a reliable fix yet....
 	#
-	MYDIR="$(cd -P "$(dirname "${0}")" && pwd)"
-	if [[ "${verbose:-0}" -eq 1 ]]
-	then
-		cd "${MYDIR}/.."
-		shellcheck -a -x -o all -f tty protocols/*.sh # cannot use the printf construct used below for non-vebose output as it destroys the terminal colors.
-		cd '-' # Goes back to previous directory before we changed to ${MYDIR}.
-	else
-		printf '%s\n' "$(cd "${MYDIR}/.." && shellcheck -a -x -o all -f gcc protocols/*.sh)"
-	fi
+	export SHELLCHECK_OPTS="${SHELLCHECK_OPTS} -e SC2312"
 fi
+shellcheck -a -x -o all -f "${format}" "${MYDIR}"/../protocols/*.sh | sed "s|${MYDIR}/../||g"
\ No newline at end of file

From c451e109fdd00169374e3c5e1b134f9e79f38bd2 Mon Sep 17 00:00:00 2001
From: Pieter Neerincx <pieter.neerincx@gmail.com>
Date: Mon, 19 Jun 2023 22:16:11 +0200
Subject: [PATCH 41/42] Trigger Jenkins.

---
 README.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/README.md b/README.md
index 6744355..bfe8604 100644
--- a/README.md
+++ b/README.md
@@ -99,3 +99,4 @@ Navigate to jobs folder. The location of the jobs folder will be outputted at th
 ```BASH
 bash submit.sh
 ```
+

From a290e9a1b94bdaa7ac3c4303fcec9deb8dee4ade Mon Sep 17 00:00:00 2001
From: Pieter Neerincx <pieter.neerincx@gmail.com>
Date: Tue, 20 Jun 2023 14:33:39 +0200
Subject: [PATCH 42/42] Removed Calculon from checkEnvironment.sh.

---
 checkEnvironment.sh | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/checkEnvironment.sh b/checkEnvironment.sh
index f05d6d2..d8f8a64 100755
--- a/checkEnvironment.sh
+++ b/checkEnvironment.sh
@@ -16,12 +16,8 @@ elif [ "${HOST}" == "leucine-zipper.gcc.rug.nl" ]
 then
 	ENVIRONMENT_PARAMETERS="leucine-zipper"
 	TMPDIR="tmp06"
-elif [ "${HOST}" == "calculon" ]
-then
-	ENVIRONMENT_PARAMETERS="calculon"
-	TMPDIR="tmp04"
 else
-	echo "Unknown host: running is only possible on calculon, zinc-finger or leucine-zipper."
+	echo "Unknown host: running is only possible on zinc-finger or leucine-zipper."
 fi
 
 THISDIR=$(pwd)