From 7a0560f5dd2c88154f5f5560141af0de80924ebf Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Sun, 13 Sep 2020 21:31:47 -0500
Subject: [PATCH] Use channel
---
workflow/rna-seq.nf | 12 ++++++------
1 file changed, 6 insertions(+), 6 deletions(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index ba0d832..04bcfa9 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -383,8 +383,8 @@ process getRefInfer {
tag "${refName}"
input:
- path credential, stageAs: "credential.json" from deriva_getRefInfer
- path script_refDataInfer
+ path credential, stageAs: "credential.json" from deriva_getRefInfer.collect()
+ path script_refDataInfer.collect()
val refName from referenceInfer
output:
@@ -439,9 +439,9 @@ process getRefInfer {
GENCODE=\$(echo \${references} | grep -o ${refName}.* | cut -d '.' -f3)
query=\$(echo 'https://${referenceBase}/ermrest/catalog/2/entity/RNASeq:Reference_Genome/Reference_Version='\${GRCv}'.'\${GRCp}'/Annotation_Version=GENCODE%20'\${GENCODE})
curl --request GET \${query} > refQuery.json
- refURL=\$(python ./workflow/scripts/extractRefData.py --returnParam URL)
+ refURL=\$(python extractRefData.py --returnParam URL)
loc=\$(dirname \${refURL})
- fName=\$(python ./workflow/scripts/extractRefData.py --returnParam fName)
+ fName=\$(python extractRefData.py --returnParam fName)
fName=\${fName%.*}
if [ "\${loc}" = "/hatrac/*" ]; then echo "LOG: Reference not present in hatrac"; exit 1; fi
filename=\$(echo \$(basename \${refURL}) | grep -oP '.*(?=:)')
@@ -779,9 +779,9 @@ process getRef {
GENCODE=\$(echo \${references} | grep -o ${refName}.* | cut -d '.' -f3)
query=\$(echo 'https://${referenceBase}/ermrest/catalog/2/entity/RNASeq:Reference_Genome/Reference_Version='\${GRCv}'.'\${GRCp}'/Annotation_Version=GENCODE%20'\${GENCODE})
curl --request GET \${query} > refQuery.json
- refURL=\$(python ./workflow/scripts/extractRefData.py --returnParam URL)
+ refURL=\$(python extractRefData.py --returnParam URL)
loc=\$(dirname \${refURL})
- fName=\$(python ./workflow/scripts/extractRefData.py --returnParam fName)
+ fName=\$(python extractRefData.py --returnParam fName)
fName=\${fName%.*}
if [ "\${loc}" = "/hatrac/*" ]; then echo "LOG: Reference not present in hatrac"; exit 1; fi
filename=\$(echo \$(basename \${refURL}) | grep -oP '.*(?=:)')
--
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