From a0719cd94f9e2fb4cb16ce2f342083bf23b3cac9 Mon Sep 17 00:00:00 2001
From: RoanKanninga <roankanninga@gmail.com>
Date: Thu, 24 Aug 2023 10:59:48 +0200
Subject: [PATCH 1/8] fixing issue where Darwin tool cannot handle decimals

---
 protocols/CoverageCalculations_gvcf.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/protocols/CoverageCalculations_gvcf.sh b/protocols/CoverageCalculations_gvcf.sh
index e56c8bc5..bee21e2c 100755
--- a/protocols/CoverageCalculations_gvcf.sh
+++ b/protocols/CoverageCalculations_gvcf.sh
@@ -125,7 +125,7 @@ then
 			
 			grep -v "NC_001422.1" "${intermediateDir}/${externalSampleID}.${perBase}.coveragePerBase.txt" > "${intermediateDir}/${externalSampleID}.${perBase}.coveragePerBase.txt.tmp"
 			echo "phiX is removed for ${externalSampleID}.${perBase} perBase" 
-			mv -v "${intermediateDir}/${externalSampleID}.${perBase}.coveragePerBase.txt.tmp" "${projectResultsDir}/coverage/CoveragePerBase/${Gender,,}/${externalSampleID}.${perBase}.coveragePerBase.txt"
+			awk '{if (NR>1){printf "%s\t%s\t%s\t%s\t%.0f\t%s\t%s\t%s\t%s\n",$1,$2,$3,$4,$5,$6,$7,$8,$9}else {print $0}}' "${intermediateDir}/${externalSampleID}.${perBase}.coveragePerBase.txt.tmp" > "${projectResultsDir}/coverage/CoveragePerBase/${Gender,,}/${externalSampleID}.${perBase}.coveragePerBase.txt"
 			
 			echo "coveragePerTarget file can be found here: ${projectResultsDir}/coverage/CoveragePerBase/${Gender,,}/${externalSampleID}.${perBase}.coveragePerBase.txt"
 			

From e302f38a49fa207acb67b2f2f4c5711960cea732 Mon Sep 17 00:00:00 2001
From: RoanKanninga <roankanninga@gmail.com>
Date: Mon, 28 Aug 2023 08:49:54 +0200
Subject: [PATCH 2/8] coveragePerBase decimals has been changed back to
 original state, so it needs to change in the truth file as well

---
 ...Test_v1.coveragePerBase.selection_True.txt | 198 +++++++++---------
 1 file changed, 99 insertions(+), 99 deletions(-)

diff --git a/test/results/PlatinumSample_NA12878.NGS_DNA_Test_v1.coveragePerBase.selection_True.txt b/test/results/PlatinumSample_NA12878.NGS_DNA_Test_v1.coveragePerBase.selection_True.txt
index f2eb6aeb..320d11ce 100644
--- a/test/results/PlatinumSample_NA12878.NGS_DNA_Test_v1.coveragePerBase.selection_True.txt
+++ b/test/results/PlatinumSample_NA12878.NGS_DNA_Test_v1.coveragePerBase.selection_True.txt
@@ -1,100 +1,100 @@
 Index	Chr	Chr Position Start	Description	Min Counts	CDS	Contig
-1	2	197550	AC079779.7	33.0	CDS	1
-2	2	197551	AC079779.7	33.0	CDS	1
-3	2	197552	AC079779.7	33.0	CDS	1
-4	2	197553	AC079779.7	33.0	CDS	1
-5	2	197554	AC079779.7	33.0	CDS	1
-6	2	197555	AC079779.7	33.0	CDS	1
-7	2	197556	AC079779.7	33.0	CDS	1
-8	2	197557	AC079779.7	33.0	CDS	1
-9	2	197558	AC079779.7	33.0	CDS	1
-10	2	197559	AC079779.7	33.0	CDS	1
-11	2	197560	AC079779.7	33.0	CDS	1
-12	2	197561	AC079779.7	33.0	CDS	1
-13	2	197562	AC079779.7	33.0	CDS	1
-14	2	197563	AC079779.7	33.0	CDS	1
-15	2	197564	AC079779.7	36.0	CDS	1
-16	2	197565	AC079779.7	36.0	CDS	1
-17	2	197566	AC079779.7	36.0	CDS	1
-18	2	197567	AC079779.7	36.0	CDS	1
-19	2	197568	AC079779.7	31.0	CDS	1
-20	2	197569	AC079779.7	31.0	CDS	1
-21	2	197570	AC079779.7	31.0	CDS	1
-22	2	197571	AC079779.7	31.0	CDS	1
-23	2	197572	AC079779.7	31.0	CDS	1
-24	2	197573	AC079779.7	31.0	CDS	1
-25	2	197574	AC079779.7	31.0	CDS	1
-26	2	197575	AC079779.7	31.0	CDS	1
-27	2	197576	AC079779.7	31.0	CDS	1
-28	2	197577	AC079779.7	31.0	CDS	1
-29	2	197578	AC079779.7	31.0	CDS	1
-30	2	197579	AC079779.7	31.0	CDS	1
-31	2	197580	AC079779.7	31.0	CDS	1
-32	2	197581	AC079779.7	31.0	CDS	1
-33	2	197582	AC079779.7	31.0	CDS	1
-34	2	197583	AC079779.7	31.0	CDS	1
-35	2	197584	AC079779.7	28.0	CDS	1
-36	2	197585	AC079779.7	28.0	CDS	1
-37	2	197586	AC079779.7	28.0	CDS	1
-38	2	197587	AC079779.7	28.0	CDS	1
-39	2	197588	AC079779.7	28.0	CDS	1
-40	2	197589	AC079779.7	28.0	CDS	1
-41	2	197590	AC079779.7	28.0	CDS	1
-42	2	197591	AC079779.7	28.0	CDS	1
-43	2	197592	AC079779.7	28.0	CDS	1
-44	2	197593	AC079779.7	27.0	CDS	1
-45	2	197594	AC079779.7	26.0	CDS	1
-46	2	197595	AC079779.7	26.0	CDS	1
-47	2	197596	AC079779.7	26.0	CDS	1
-48	2	197597	AC079779.7	25.0	CDS	1
-49	2	197598	AC079779.7	25.0	CDS	1
-52329	Y	2803782	ZFY	0.0	CDS	1
-52330	Y	2803783	ZFY	0.0	CDS	1
-52331	Y	2803784	ZFY	0.0	CDS	1
-52332	Y	2803785	ZFY	0.0	CDS	1
-52333	Y	2803786	ZFY	0.0	CDS	1
-52334	Y	2803787	ZFY	0.0	CDS	1
-52335	Y	2803788	ZFY	0.0	CDS	1
-52336	Y	2803789	ZFY	0.0	CDS	1
-52337	Y	2803790	ZFY	0.0	CDS	1
-52338	Y	2803791	ZFY	0.0	CDS	1
-52339	Y	2803792	ZFY	0.0	CDS	1
-52340	Y	2803793	ZFY	0.0	CDS	1
-52341	Y	2803794	ZFY	0.0	CDS	1
-52342	Y	2803795	ZFY	0.0	CDS	1
-52343	Y	2803796	ZFY	0.0	CDS	1
-52344	Y	2803797	ZFY	0.0	CDS	1
-52345	Y	2803798	ZFY	0.0	CDS	1
-52346	Y	2803799	ZFY	0.0	CDS	1
-52347	Y	2803800	ZFY	0.0	CDS	1
-52348	Y	2803801	ZFY	0.0	CDS	1
-52349	Y	2803802	ZFY	0.0	CDS	1
-52350	Y	2803803	ZFY	0.0	CDS	1
-52351	Y	2803804	ZFY	0.0	CDS	1
-52352	Y	2803805	ZFY	0.0	CDS	1
-52353	Y	2803806	ZFY	0.0	CDS	1
-52354	Y	2803807	ZFY	0.0	CDS	1
-52355	Y	2803808	ZFY	0.0	CDS	1
-52356	Y	2803809	ZFY	0.0	CDS	1
-52357	Y	2803810	ZFY	0.0	CDS	1
-52358	Y	2803811	ZFY	0.0	CDS	1
-52359	Y	2803812	ZFY	0.0	CDS	1
-52360	Y	2803813	ZFY	0.0	CDS	1
-52361	Y	2803814	ZFY	0.0	CDS	1
-52362	Y	2803815	ZFY	0.0	CDS	1
-52363	Y	2803816	ZFY	0.0	CDS	1
-52364	Y	2803817	ZFY	0.0	CDS	1
-52365	Y	2803818	ZFY	0.0	CDS	1
-52366	Y	2803819	ZFY	0.0	CDS	1
-52367	Y	2803820	ZFY	0.0	CDS	1
-52368	Y	2803821	ZFY	0.0	CDS	1
-52369	Y	2803822	ZFY	0.0	CDS	1
-52370	Y	2803823	ZFY	0.0	CDS	1
-52371	Y	2803824	ZFY	0.0	CDS	1
-52372	Y	2803825	ZFY	0.0	CDS	1
-52373	Y	2803826	ZFY	0.0	CDS	1
-52374	Y	2803827	ZFY	0.0	CDS	1
-52375	Y	2803828	ZFY	0.0	CDS	1
-52376	Y	2803829	ZFY	0.0	CDS	1
-52377	Y	2803830	ZFY	0.0	CDS	1
-52378	Y	2803831	ZFY	0.0	CDS	1
+1	2	197550	AC079779.7	33	CDS	1		
+2	2	197551	AC079779.7	33	CDS	1		
+3	2	197552	AC079779.7	33	CDS	1		
+4	2	197553	AC079779.7	33	CDS	1		
+5	2	197554	AC079779.7	33	CDS	1		
+6	2	197555	AC079779.7	33	CDS	1		
+7	2	197556	AC079779.7	33	CDS	1		
+8	2	197557	AC079779.7	33	CDS	1		
+9	2	197558	AC079779.7	33	CDS	1		
+10	2	197559	AC079779.7	33	CDS	1		
+11	2	197560	AC079779.7	33	CDS	1		
+12	2	197561	AC079779.7	33	CDS	1		
+13	2	197562	AC079779.7	33	CDS	1		
+14	2	197563	AC079779.7	33	CDS	1		
+15	2	197564	AC079779.7	36	CDS	1		
+16	2	197565	AC079779.7	36	CDS	1		
+17	2	197566	AC079779.7	36	CDS	1		
+18	2	197567	AC079779.7	36	CDS	1		
+19	2	197568	AC079779.7	31	CDS	1		
+20	2	197569	AC079779.7	31	CDS	1		
+21	2	197570	AC079779.7	31	CDS	1		
+22	2	197571	AC079779.7	31	CDS	1		
+23	2	197572	AC079779.7	31	CDS	1		
+24	2	197573	AC079779.7	31	CDS	1		
+25	2	197574	AC079779.7	31	CDS	1		
+26	2	197575	AC079779.7	31	CDS	1		
+27	2	197576	AC079779.7	31	CDS	1		
+28	2	197577	AC079779.7	31	CDS	1		
+29	2	197578	AC079779.7	31	CDS	1		
+30	2	197579	AC079779.7	31	CDS	1		
+31	2	197580	AC079779.7	31	CDS	1		
+32	2	197581	AC079779.7	31	CDS	1		
+33	2	197582	AC079779.7	31	CDS	1		
+34	2	197583	AC079779.7	31	CDS	1		
+35	2	197584	AC079779.7	28	CDS	1		
+36	2	197585	AC079779.7	28	CDS	1		
+37	2	197586	AC079779.7	28	CDS	1		
+38	2	197587	AC079779.7	28	CDS	1		
+39	2	197588	AC079779.7	28	CDS	1		
+40	2	197589	AC079779.7	28	CDS	1		
+41	2	197590	AC079779.7	28	CDS	1		
+42	2	197591	AC079779.7	28	CDS	1		
+43	2	197592	AC079779.7	28	CDS	1		
+44	2	197593	AC079779.7	27	CDS	1		
+45	2	197594	AC079779.7	26	CDS	1		
+46	2	197595	AC079779.7	26	CDS	1		
+47	2	197596	AC079779.7	26	CDS	1		
+48	2	197597	AC079779.7	25	CDS	1		
+49	2	197598	AC079779.7	25	CDS	1		
+52329	Y	2803782	ZFY	0	CDS	1		
+52330	Y	2803783	ZFY	0	CDS	1		
+52331	Y	2803784	ZFY	0	CDS	1		
+52332	Y	2803785	ZFY	0	CDS	1		
+52333	Y	2803786	ZFY	0	CDS	1		
+52334	Y	2803787	ZFY	0	CDS	1		
+52335	Y	2803788	ZFY	0	CDS	1		
+52336	Y	2803789	ZFY	0	CDS	1		
+52337	Y	2803790	ZFY	0	CDS	1		
+52338	Y	2803791	ZFY	0	CDS	1		
+52339	Y	2803792	ZFY	0	CDS	1		
+52340	Y	2803793	ZFY	0	CDS	1		
+52341	Y	2803794	ZFY	0	CDS	1		
+52342	Y	2803795	ZFY	0	CDS	1		
+52343	Y	2803796	ZFY	0	CDS	1		
+52344	Y	2803797	ZFY	0	CDS	1		
+52345	Y	2803798	ZFY	0	CDS	1		
+52346	Y	2803799	ZFY	0	CDS	1		
+52347	Y	2803800	ZFY	0	CDS	1		
+52348	Y	2803801	ZFY	0	CDS	1		
+52349	Y	2803802	ZFY	0	CDS	1		
+52350	Y	2803803	ZFY	0	CDS	1		
+52351	Y	2803804	ZFY	0	CDS	1		
+52352	Y	2803805	ZFY	0	CDS	1		
+52353	Y	2803806	ZFY	0	CDS	1		
+52354	Y	2803807	ZFY	0	CDS	1		
+52355	Y	2803808	ZFY	0	CDS	1		
+52356	Y	2803809	ZFY	0	CDS	1		
+52357	Y	2803810	ZFY	0	CDS	1		
+52358	Y	2803811	ZFY	0	CDS	1		
+52359	Y	2803812	ZFY	0	CDS	1		
+52360	Y	2803813	ZFY	0	CDS	1		
+52361	Y	2803814	ZFY	0	CDS	1		
+52362	Y	2803815	ZFY	0	CDS	1		
+52363	Y	2803816	ZFY	0	CDS	1		
+52364	Y	2803817	ZFY	0	CDS	1		
+52365	Y	2803818	ZFY	0	CDS	1		
+52366	Y	2803819	ZFY	0	CDS	1		
+52367	Y	2803820	ZFY	0	CDS	1		
+52368	Y	2803821	ZFY	0	CDS	1		
+52369	Y	2803822	ZFY	0	CDS	1		
+52370	Y	2803823	ZFY	0	CDS	1		
+52371	Y	2803824	ZFY	0	CDS	1		
+52372	Y	2803825	ZFY	0	CDS	1		
+52373	Y	2803826	ZFY	0	CDS	1		
+52374	Y	2803827	ZFY	0	CDS	1		
+52375	Y	2803828	ZFY	0	CDS	1		
+52376	Y	2803829	ZFY	0	CDS	1		
+52377	Y	2803830	ZFY	0	CDS	1		
+52378	Y	2803831	ZFY	0	CDS	1		

From b16cc7c93ad8d8bc82050211effa83423463713d Mon Sep 17 00:00:00 2001
From: RoanKanninga <roankanninga@gmail.com>
Date: Wed, 30 Aug 2023 12:42:06 +0200
Subject: [PATCH 3/8] force build

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

diff --git a/README.md b/README.md
index 89e7a6fe..ff0f2af3 100755
--- a/README.md
+++ b/README.md
@@ -20,4 +20,3 @@ Based on quality thresholds from the GATK "best practices"<sup>5</sup>, the SNPs
 3. Tarasov A et al. (2015). Sambamba: Fast processing of NGS alignment formats.<br/>
 4. McKenna A et al. (2010). The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.<br/>
 5. Van der Auwera GA et al. (2013). From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline.<br/>
-

From 8dc0eae9a088bcfddc5c2b3ecf7dd6068ede456e Mon Sep 17 00:00:00 2001
From: RoanKanninga <roankanninga@gmail.com>
Date: Wed, 30 Aug 2023 13:19:16 +0200
Subject: [PATCH 4/8] trigger builkd

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

diff --git a/README.md b/README.md
index ff0f2af3..89e7a6fe 100755
--- a/README.md
+++ b/README.md
@@ -20,3 +20,4 @@ Based on quality thresholds from the GATK "best practices"<sup>5</sup>, the SNPs
 3. Tarasov A et al. (2015). Sambamba: Fast processing of NGS alignment formats.<br/>
 4. McKenna A et al. (2010). The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.<br/>
 5. Van der Auwera GA et al. (2013). From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline.<br/>
+

From 3b9ce8c123abb9abe186055fde028848f72e63da Mon Sep 17 00:00:00 2001
From: RoanKanninga <roankanninga@gmail.com>
Date: Wed, 30 Aug 2023 16:57:13 +0200
Subject: [PATCH 5/8] repairing this HUUUUGE bug in git where changing the
 capitalization of your filenames should never occur once it is in the repo
 already

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

diff --git a/workflow_DRAGEN.csv b/workflow_DRAGEN.csv
index 3d765e6d..eaf7b04d 100644
--- a/workflow_DRAGEN.csv
+++ b/workflow_DRAGEN.csv
@@ -1,6 +1,6 @@
 step,protocol,dependencies
 s01_PrepareDragenData,protocols/PrepareDragenData.sh,
-s01b_processDragenTrendAnalysis,protocols/processDragenTrendAnalysis.sh,s01_PrepareDragenData
+s01b_processDragenTrendanalysis,protocols/processDragenTrendanalysis.sh,s01_PrepareDragenData
 s02_CoverageCalculations,protocols/CoverageCalculations_gvcf.sh,s01_PrepareDragenData;variantCalls=sampleDragenRawVariantCalls;merge=noMerge
 s03_AnnotateVcf,protocols/AnnotateVcf_perSample.sh,s01_PrepareDragenData;variantCalls=sampleDragenVariantCalls
 s04_SnpEff,protocols/SnpEff_perSample.sh,s03_AnnotateVcf

From dc34459d9968593c8a4834e61d23543c0f35fc92 Mon Sep 17 00:00:00 2001
From: RoanKanninga <roankanninga@gmail.com>
Date: Wed, 30 Aug 2023 17:05:40 +0200
Subject: [PATCH 6/8] fix capitalization issue

---
 ...ssDragenTrendanalysis.sh => ProcessDragenTrendAnalysis.sh} | 0
 workflow_DRAGEN.csv                                           | 4 ++--
 2 files changed, 2 insertions(+), 2 deletions(-)
 rename protocols/{processDragenTrendanalysis.sh => ProcessDragenTrendAnalysis.sh} (100%)

diff --git a/protocols/processDragenTrendanalysis.sh b/protocols/ProcessDragenTrendAnalysis.sh
similarity index 100%
rename from protocols/processDragenTrendanalysis.sh
rename to protocols/ProcessDragenTrendAnalysis.sh
diff --git a/workflow_DRAGEN.csv b/workflow_DRAGEN.csv
index eaf7b04d..75d26de0 100644
--- a/workflow_DRAGEN.csv
+++ b/workflow_DRAGEN.csv
@@ -1,9 +1,9 @@
 step,protocol,dependencies
 s01_PrepareDragenData,protocols/PrepareDragenData.sh,
-s01b_processDragenTrendanalysis,protocols/processDragenTrendanalysis.sh,s01_PrepareDragenData
+s01b_ProcessDragenTrendAnalysis,protocols/ProcessDragenTrendAnalysis.sh,s01_PrepareDragenData
 s02_CoverageCalculations,protocols/CoverageCalculations_gvcf.sh,s01_PrepareDragenData;variantCalls=sampleDragenRawVariantCalls;merge=noMerge
 s03_AnnotateVcf,protocols/AnnotateVcf_perSample.sh,s01_PrepareDragenData;variantCalls=sampleDragenVariantCalls
 s04_SnpEff,protocols/SnpEff_perSample.sh,s03_AnnotateVcf
 s08_Gavin,protocols/Gavin.sh,s04_SnpEff;inputFile=sampleVariantCallsSnpEff_Annotated
 s09_ReheaderVcf,protocols/ReheaderVCF.sh,s08_Gavin
-s10_PipelineFinished,protocols/PipelineFinished.sh,s01b_processDragenTrendAnalysis;s02_CoverageCalculations;s09_ReheaderVcf
\ No newline at end of file
+s10_PipelineFinished,protocols/PipelineFinished.sh,s01b_processDragenTrendAnalysis;s02_CoverageCalculations;s09_ReheaderVcf

From 6b88f30500bde38dfba8d1a17c0456b38092e2f8 Mon Sep 17 00:00:00 2001
From: RoanKanninga <roankanninga@gmail.com>
Date: Wed, 30 Aug 2023 17:14:40 +0200
Subject: [PATCH 7/8] removing 2 empty tabs at the end of the coveragePerBase
 output

---
 protocols/CoverageCalculations_gvcf.sh        |   2 +-
 ...Test_v1.coveragePerBase.selection_True.txt | 198 +++++++++---------
 2 files changed, 100 insertions(+), 100 deletions(-)

diff --git a/protocols/CoverageCalculations_gvcf.sh b/protocols/CoverageCalculations_gvcf.sh
index bee21e2c..1ef1cc6a 100755
--- a/protocols/CoverageCalculations_gvcf.sh
+++ b/protocols/CoverageCalculations_gvcf.sh
@@ -125,7 +125,7 @@ then
 			
 			grep -v "NC_001422.1" "${intermediateDir}/${externalSampleID}.${perBase}.coveragePerBase.txt" > "${intermediateDir}/${externalSampleID}.${perBase}.coveragePerBase.txt.tmp"
 			echo "phiX is removed for ${externalSampleID}.${perBase} perBase" 
-			awk '{if (NR>1){printf "%s\t%s\t%s\t%s\t%.0f\t%s\t%s\t%s\t%s\n",$1,$2,$3,$4,$5,$6,$7,$8,$9}else {print $0}}' "${intermediateDir}/${externalSampleID}.${perBase}.coveragePerBase.txt.tmp" > "${projectResultsDir}/coverage/CoveragePerBase/${Gender,,}/${externalSampleID}.${perBase}.coveragePerBase.txt"
+			awk '{if (NR>1){printf "%s\t%s\t%s\t%s\t%.0f\t%s\t%s\n",$1,$2,$3,$4,$5,$6,$7}else {print $0}}' "${intermediateDir}/${externalSampleID}.${perBase}.coveragePerBase.txt.tmp" > "${projectResultsDir}/coverage/CoveragePerBase/${Gender,,}/${externalSampleID}.${perBase}.coveragePerBase.txt"
 			
 			echo "coveragePerTarget file can be found here: ${projectResultsDir}/coverage/CoveragePerBase/${Gender,,}/${externalSampleID}.${perBase}.coveragePerBase.txt"
 			
diff --git a/test/results/PlatinumSample_NA12878.NGS_DNA_Test_v1.coveragePerBase.selection_True.txt b/test/results/PlatinumSample_NA12878.NGS_DNA_Test_v1.coveragePerBase.selection_True.txt
index 320d11ce..d615b866 100644
--- a/test/results/PlatinumSample_NA12878.NGS_DNA_Test_v1.coveragePerBase.selection_True.txt
+++ b/test/results/PlatinumSample_NA12878.NGS_DNA_Test_v1.coveragePerBase.selection_True.txt
@@ -1,100 +1,100 @@
 Index	Chr	Chr Position Start	Description	Min Counts	CDS	Contig
-1	2	197550	AC079779.7	33	CDS	1		
-2	2	197551	AC079779.7	33	CDS	1		
-3	2	197552	AC079779.7	33	CDS	1		
-4	2	197553	AC079779.7	33	CDS	1		
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-52366	Y	2803819	ZFY	0	CDS	1		
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+1	2	197550	AC079779.7	33	CDS	1
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+3	2	197552	AC079779.7	33	CDS	1
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+9	2	197558	AC079779.7	33	CDS	1
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+11	2	197560	AC079779.7	33	CDS	1
+12	2	197561	AC079779.7	33	CDS	1
+13	2	197562	AC079779.7	33	CDS	1
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+15	2	197564	AC079779.7	36	CDS	1
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+17	2	197566	AC079779.7	36	CDS	1
+18	2	197567	AC079779.7	36	CDS	1
+19	2	197568	AC079779.7	31	CDS	1
+20	2	197569	AC079779.7	31	CDS	1
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+25	2	197574	AC079779.7	31	CDS	1
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+29	2	197578	AC079779.7	31	CDS	1
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+31	2	197580	AC079779.7	31	CDS	1
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+33	2	197582	AC079779.7	31	CDS	1
+34	2	197583	AC079779.7	31	CDS	1
+35	2	197584	AC079779.7	28	CDS	1
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+37	2	197586	AC079779.7	28	CDS	1
+38	2	197587	AC079779.7	28	CDS	1
+39	2	197588	AC079779.7	28	CDS	1
+40	2	197589	AC079779.7	28	CDS	1
+41	2	197590	AC079779.7	28	CDS	1
+42	2	197591	AC079779.7	28	CDS	1
+43	2	197592	AC079779.7	28	CDS	1
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+47	2	197596	AC079779.7	26	CDS	1
+48	2	197597	AC079779.7	25	CDS	1
+49	2	197598	AC079779.7	25	CDS	1
+52329	Y	2803782	ZFY	0	CDS	1
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+52369	Y	2803822	ZFY	0	CDS	1
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+52372	Y	2803825	ZFY	0	CDS	1
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+52374	Y	2803827	ZFY	0	CDS	1
+52375	Y	2803828	ZFY	0	CDS	1
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+52378	Y	2803831	ZFY	0	CDS	1

From 967e2d9dff751cd2f59ec9d3e4b5a127c87a5e0d Mon Sep 17 00:00:00 2001
From: RoanKanninga <roankanninga@gmail.com>
Date: Wed, 30 Aug 2023 17:17:39 +0200
Subject: [PATCH 8/8] update workflow dependency

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

diff --git a/workflow_DRAGEN.csv b/workflow_DRAGEN.csv
index 75d26de0..bdcadb01 100644
--- a/workflow_DRAGEN.csv
+++ b/workflow_DRAGEN.csv
@@ -6,4 +6,4 @@ s03_AnnotateVcf,protocols/AnnotateVcf_perSample.sh,s01_PrepareDragenData;variant
 s04_SnpEff,protocols/SnpEff_perSample.sh,s03_AnnotateVcf
 s08_Gavin,protocols/Gavin.sh,s04_SnpEff;inputFile=sampleVariantCallsSnpEff_Annotated
 s09_ReheaderVcf,protocols/ReheaderVCF.sh,s08_Gavin
-s10_PipelineFinished,protocols/PipelineFinished.sh,s01b_processDragenTrendAnalysis;s02_CoverageCalculations;s09_ReheaderVcf
+s10_PipelineFinished,protocols/PipelineFinished.sh,s01b_ProcessDragenTrendAnalysis;s02_CoverageCalculations;s09_ReheaderVcf