From b3128fbb48f967057cd057f2fa9d23714ffdb055 Mon Sep 17 00:00:00 2001
From: kohleman <kohleman>
Date: Thu, 15 Dec 2016 13:39:47 +0000
Subject: [PATCH] handle the case of re-registering a single lane
SVN: 37511
---
.../source/BDS/analysis_bcl2fastq.bds | 13 ++++++++-----
1 file changed, 8 insertions(+), 5 deletions(-)
diff --git a/deep_sequencing_unit/source/BDS/analysis_bcl2fastq.bds b/deep_sequencing_unit/source/BDS/analysis_bcl2fastq.bds
index 3d5ddc8329d..7085666c1b9 100755
--- a/deep_sequencing_unit/source/BDS/analysis_bcl2fastq.bds
+++ b/deep_sequencing_unit/source/BDS/analysis_bcl2fastq.bds
@@ -632,8 +632,6 @@ void rsyncDemultiplexedFiles (int [] laneCount) {
string newFolderName = "Undetermined_" + cleanString(fcName) + "_" + lane
#Undetermined_000000000_AH4PH_1
string newFolderPath = searchFolder + "/" + newFolderName
- newFolderPath.mkdir()
- print("Created $newFolderPath\n")
# Assuming it is only one lane
if (listOfLanes.size() == 1 && listOfLanes[0] == 1) {
@@ -643,9 +641,15 @@ void rsyncDemultiplexedFiles (int [] laneCount) {
filesPerLane = searchFolder.dir("*L00" + lane + "*.fastq.gz")
}
+ newFolderPath.mkdir()
+ print("Created $newFolderPath\n")
+
for (string fastqFile : filesPerLane) {
- sys mv "$searchFolder/$fastqFile" "$searchFolder/$newFolderName"
- sys ln -s "$searchFolder/$newFolderName/$fastqFile" "$searchFolder/$fastqFile"
+ string moveAndLinkID task ( canFail := true, cpus := 1 ){
+ # sys echo "$searchFolder/$fastqFile" "$searchFolder/$newFolderName"
+ sys [[ -f "$searchFolder/$fastqFile" ]] && mv "$searchFolder/$fastqFile" "$searchFolder/$newFolderName/"
+ sys [[ ! -f "$searchFolder/$fastqFile" ]] && ln -s "$searchFolder/$newFolderName/$fastqFile" "$searchFolder/$fastqFile"
+ }
}
sys chmod -R 774 "$newFolderPath"
@@ -674,7 +678,6 @@ void rsyncDemultiplexedFiles (int [] laneCount) {
"$nohupFile", \
"$unalignedData/$sampleFolder", \
"$unalignedData/$marker$sampleFolder")
-
}
}
}
--
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