diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf index 4eb3a93dc00c808cf0b40e64ef168fd8dea77295..d08cd3918cdd1fa7c73d3f3d0be2116b797a4b77 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}