From 466e814a50d679348947e9191c6b441d46a07653 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Sat, 13 Feb 2021 11:59:40 -0600
Subject: [PATCH] Link deriva credentials for upload processed files and fix
logs
---
rna-seq.nf | 20 +++++++++++++-------
1 file changed, 13 insertions(+), 7 deletions(-)
diff --git a/rna-seq.nf b/rna-seq.nf
index 1fe526c..53e5a51 100644
--- a/rna-seq.nf
+++ b/rna-seq.nf
@@ -2196,8 +2196,14 @@ process uploadProcessedFile {
script:
"""
- hostname > ${repRID}.outputBag.log
- ulimit -a >> ${repRID}.outputBag.log
+ hostname > ${repRID}.uploadProcessedFile.log
+ ulimit -a >> ${repRID}.uploadProcessedFile.log
+
+ # link credential file for authentication
+ echo -e "LOG: linking deriva credentials" >> ${repRID}.uploadProcessedFile.log
+ mkdir -p ~/.deriva
+ ln -sf `readlink -e credential.json` ~/.deriva/credential.json
+ echo -e "LOG: linked" >> ${repRID}.uploadProcessedFile.log
mkdir -p ./deriva/Seq/pipeline/${studyRID}/${executionRunRID}/
cp ${bam} ./deriva/Seq/pipeline/${studyRID}/${executionRunRID}/
@@ -2216,14 +2222,14 @@ process uploadProcessedFile {
do
python3 ${script_deleteEntry_uploadProcessedFile} -r \${rid} -t Processed_File -o ${source} -c \${cookie}
done
- echo LOG: all old processed file RIDs deleted >> ${repRID}.uploadQC.log
+ echo LOG: all old processed file RIDs deleted >> ${repRID}.uploadProcessedFile.log
fi
deriva-upload-cli --catalog 2 --token \${cookie:9} ${source} ./deriva
- echo LOG: processed files uploaded >> ${repRID}.outputBag.log
+ echo LOG: processed files uploaded >> ${repRID}.outpuploadProcessedFileutBag.log
deriva-download-cli --catalog 2 --token \${cookie:9} ${source} ${executionRunExportConfig} . rid=${executionRunRID}
- echo LOG: execution run bag downloaded >> ${repRID}.outputBag.log
+ echo LOG: execution run bag downloaded >> ${repRID}.uploadProcessedFile.log
echo -e "### Run Details" >> runDetails.md
echo -e "**Workflow URL:** https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq" >> runDetails.md
@@ -2241,7 +2247,7 @@ process uploadProcessedFile {
echo -e "**Genome Assembly Version:** \${genome} patch \${patch}" >> runDetails.md
echo -e "**Annotation Version:** GENCODE release \${annotation}" >> runDetails.md
echo -e "**Run ID:** ${repRID}" >> runDetails.md
- echo LOG: runDetails.md created >> ${repRID}.outputBag.log
+ echo LOG: runDetails.md created >> ${repRID}.uploadProcessedFile.log
unzip Execution_Run_${executionRunRID}.zip
yr=\$(date +'%Y')
@@ -2255,7 +2261,7 @@ process uploadProcessedFile {
cp ${multiqcJSON} \${loc}
bdbag ./${repRID}_Output_Bag/ --update --archiver zip --debug
- echo LOG: output bag created >> ${repRID}.outputBag.log
+ echo LOG: output bag created >> ${repRID}.uploadProcessedFile.log
"""
}
--
GitLab