From 1bdfd212d98f8a557cd6b28cba322f62c6e88785 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Thu, 17 Dec 2020 10:36:37 -0600
Subject: [PATCH] Change hatrac path upload for input/output bags
---
workflow/rna-seq.nf | 24 ++++++------------------
1 file changed, 6 insertions(+), 18 deletions(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index ccedc85..cc71d85 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -345,7 +345,9 @@ endsManual.into {
}
studyRID.into {
studyRID_aggrQC
+ studyRID_uploadInputBag
studyRID_outputBag
+ studyRID_uploadOutputBag
}
expRID.into {
expRID_aggrQC
@@ -1282,6 +1284,7 @@ process uploadInputBag {
path script_uploadInputBag
path credential, stageAs: "credential.json" from deriva_uploadInputBag
path inputBag from inputBag_uploadInputBag
+ val studyRID from studyRID_uploadInputBag
output:
path ("inputBagRID.csv") into inputBagRID_fl
@@ -1298,14 +1301,6 @@ process uploadInputBag {
mn=\$(date +'%m')
dy=\$(date +'%d')
-# if [ `deriva-hatrac-cli --host ${source} ls /hatrac/resources/rnaseq/pipeline/input_bag/ | grep -q \${yr}_\${mn}_\${dy}` ]
-# then
-# deriva-hatrac-cli --host ${source} mkdir /hatrac/resources/rnaseq/pipeline/input_bag/\${yr}_\${mn}_\${dy}
-# echo LOG: hatrac folder created - /hatrac/resources/rnaseq/pipeline/input_bag/\${yr}_\${mn}_\${dy} >> ${repRID}.uploadInputBag.log
-# else
-# echo LOG: hatrac folder already exists - /hatrac/resources/rnaseq/pipeline/input_bag/\${yr}_\${mn}_\${dy} >> ${repRID}.uploadInputBag.log
-# fi
-
file=\$(basename -a ${inputBag})
md5=\$(md5sum ./\${file} | awk '{ print \$1 }')
echo LOG: ${repRID} input bag md5 sum - \${md5} >> ${repRID}.uploadInputBag.log
@@ -1318,7 +1313,7 @@ process uploadInputBag {
cookie=\$(cat credential.json | grep -A 1 '\\"${source}\\": {' | grep -o '\\"cookie\\": \\".*\\"')
cookie=\${cookie:11:-1}
- loc=\$(deriva-hatrac-cli --host ${source} put ./\${file} /hatrac/resources/rnaseq/pipeline/input_bag/\${yr}_\${mn}_\${dy}/\${file} --parents)
+ loc=\$(deriva-hatrac-cli --host ${source} put ./\${file} /hatrac/resources/rnaseq/pipeline/input_bag/study/${studyRID}/replicate/${repRID}/\${file} --parents)
inputBag_rid=\$(python3 uploadInputBag.py -f \${file} -l \${loc} -s \${md5} -b \${size} -o ${source} -c \${cookie})
echo LOG: input bag RID uploaded - \${inputBag_rid} >> ${repRID}.uploadInputBag.log
rid=\${inputBag_rid}
@@ -1566,6 +1561,7 @@ process uploadOutputBag {
path script_uploadOutputBag
path credential, stageAs: "credential.json" from deriva_uploadOutputBag
path outputBag
+ val studyRID from studyRID_uploadOutputBag
val executionRunRID from executionRunRID_uploadOutputBag
output:
@@ -1583,14 +1579,6 @@ process uploadOutputBag {
mn=\$(date +'%m')
dy=\$(date +'%d')
-# if [ `deriva-hatrac-cli --host ${source} ls /hatrac/resources/rnaseq/pipeline/output_bag/ | grep -q \${yr}_\${mn}_\${dy}` ]
-# then
-# deriva-hatrac-cli --host ${source} mkdir /hatrac/resources/rnaseq/pipeline/output_bag/\${yr}_\${mn}_\${dy}
-# echo LOG: hatrac folder created - /hatrac/resources/rnaseq/pipeline/output_bag/\${yr}_\${mn}_\${dy} >> ${repRID}.uploadOutputBag.log
-# else
-# echo LOG: hatrac folder already exists - /hatrac/resources/rnaseq/pipeline/output_bag/\${yr}_\${mn}_\${dy} >> ${repRID}.uploadOutputBag.log
-# fi
-
file=\$(basename -a ${outputBag})
md5=\$(md5sum ./\${file} | awk '{ print \$1 }')
echo LOG: ${repRID} output bag md5 sum - \${md5} >> ${repRID}.uploadOutputBag.log
@@ -1603,7 +1591,7 @@ process uploadOutputBag {
cookie=\$(cat credential.json | grep -A 1 '\\"${source}\\": {' | grep -o '\\"cookie\\": \\".*\\"')
cookie=\${cookie:11:-1}
- loc=\$(deriva-hatrac-cli --host ${source} put ./\${file} /hatrac/resources/rnaseq/pipeline/output_bag/\${yr}_\${mn}_\${dy}/\${file} --parents)
+ loc=\$(deriva-hatrac-cli --host ${source} put ./\${file} /hatrac/resources/rnaseq/pipeline/output_bag/study/${studyRID}/replicate/${repRID}/\${file} --parents)
outputBag_rid=\$(python3 uploadOutputBag.py -e ${executionRunRID} -f \${file} -l \${loc} -s \${md5} -b \${size} -o ${source} -c \${cookie})
echo LOG: output bag RID uploaded - \${outputBag_rid} >> ${repRID}.uploadOutputBag.log
rid=\${outputBag_rid}
--
GitLab