From 6090e16c8d556a0dfbe61bdc2135417dace656b7 Mon Sep 17 00:00:00 2001
From: RoanKanninga <roankanninga@gmail.com>
Date: Thu, 17 Aug 2023 15:48:08 +0200
Subject: [PATCH 1/3] removed duplicated coverage reports

---
 protocols/CopyToResultsDir.sh | 28 ----------------------------
 1 file changed, 28 deletions(-)

diff --git a/protocols/CopyToResultsDir.sh b/protocols/CopyToResultsDir.sh
index 36de1ea2..09f24c29 100755
--- a/protocols/CopyToResultsDir.sh
+++ b/protocols/CopyToResultsDir.sh
@@ -131,20 +131,6 @@ do
 	rsync -a "${intermediateDir}/${sa}.final.vcf.gz.tbi" "${projectResultsDir}/variants/"
 	printf '.'
 	
-	mapfile -t coveragePerBaseFiles < <(find "${intermediateDir}" -name "${sa}*.coveragePerBase.txt")
-	if [[ "${#coveragePerBaseFiles[@]}" -eq '0' ]]
-	then
-		echo "there are no coveragePerBase files for sample: ${sa}"
-		continue
-	else
-		for coveragePerBaseFile in "${coveragePerBaseFiles[@]}"
-		do
-			rsync -a "${coveragePerBaseFile}" "${projectResultsDir}/coverage/CoveragePerBase/"
-			printf '.'
-		done
-	fi
-	
-
 	## copy the rejected samples (with less 90% of the targets with > 20x coverage)
 	mapfile -t rejectedSamples < <(find "${intermediateDir}" -name "${sa}*.rejected")
 	if [[ "${#rejectedSamples[@]}" -eq '0' ]]
@@ -158,24 +144,10 @@ do
 		done
 		cat "${intermediateDir}/${sa}"*.rejected > "${projectResultsDir}/coverage/rejectedSamplesResult.txt"
 	fi
-	
-	mapfile -t coveragePerTargetFiles < <(find "${intermediateDir}" -name "${sa}*.coveragePerTarget.txt")
-	if [[ "${#coveragePerTargetFiles[@]}" -eq '0' ]]
-	then
-		echo "there are no coveragePerTarget files for sample: ${sa}"
-		continue
-	else
-		for coveragePerTargetFile in "${coveragePerTargetFiles[@]}"
-		do
-			rsync -a "${coveragePerTargetFile}" "${projectResultsDir}/coverage/CoveragePerTarget/"
-			printf '.'
-		done
-	fi
 
 done
 printf " finished\n"
 
-
 # print README.txt files
 printf "Copying QC report to results directory "
 

From 3a61ffa1890650734b32af5c8a6fa6f58961d43f Mon Sep 17 00:00:00 2001
From: RoanKanninga <roankanninga@gmail.com>
Date: Mon, 21 Aug 2023 09:54:25 +0200
Subject: [PATCH 2/3] update comment line

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

diff --git a/protocols/CopyToResultsDir.sh b/protocols/CopyToResultsDir.sh
index 09f24c29..6f98b71e 100755
--- a/protocols/CopyToResultsDir.sh
+++ b/protocols/CopyToResultsDir.sh
@@ -121,7 +121,7 @@ do
 done
 printf '%s' " finished\n"
 
-#copy vcf file + coveragePerBase.txt + gender determination
+#copy vcf file
 printf "Copying vcf files, gender determination, coverage per base and per target files "
 for sa in "${UNIQUESAMPLES[@]}"
 do

From dec35a2b5f298f1d3394a5064f72f7c8e2aa03e7 Mon Sep 17 00:00:00 2001
From: RoanKanninga <roankanninga@gmail.com>
Date: Mon, 21 Aug 2023 10:38:20 +0200
Subject: [PATCH 3/3] update comment line

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

diff --git a/protocols/CopyToResultsDir.sh b/protocols/CopyToResultsDir.sh
index 6f98b71e..20c50c12 100755
--- a/protocols/CopyToResultsDir.sh
+++ b/protocols/CopyToResultsDir.sh
@@ -122,7 +122,7 @@ done
 printf '%s' " finished\n"
 
 #copy vcf file
-printf "Copying vcf files, gender determination, coverage per base and per target files "
+printf "Copying vcf files"
 for sa in "${UNIQUESAMPLES[@]}"
 do