From b15b2201ecaee49b4092549dca6f5e3f221f9f94 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Tue, 26 Jan 2021 11:31:19 -0600
Subject: [PATCH] URLify hatrac location for outputBag
---
workflow/rna-seq.nf | 5 +++++
1 file changed, 5 insertions(+)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 4eb3a93..d08cd39 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -2215,6 +2215,11 @@ process uploadOutputBag {
echo LOG: ${repRID} output bag size - \${size} bytes >> ${repRID}.uploadOutputBag.log
loc=\$(deriva-hatrac-cli --host ${source} put ./\${file} /hatrac/resources/rnaseq/pipeline/output_bag/study/${studyRID}/replicate/${repRID}/\${file} --parents)
+ echo LOG: output bag uploaded - \${loc} >> ${repRID}.uploadOutputBag.log
+ # url-ify the location
+ loc=${loc//\//%2F}
+ loc=${loc//:/%3A}
+ loc=${loc// /@20}
cookie=\$(cat credential.json | grep -A 1 '\\"${source}\\": {' | grep -o '\\"cookie\\": \\".*\\"')
cookie=\${cookie:11:-1}
--
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