diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf index d08cd3918cdd1fa7c73d3f3d0be2116b797a4b77..c984b25a561397be17448675fe07d1f9bae86ec7 100644 --- a/workflow/rna-seq.nf +++ b/workflow/rna-seq.nf @@ -2217,9 +2217,9 @@ process uploadOutputBag { 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} + loc=\${loc//\//%2F} + loc=\${loc//:/%3A} + loc=\${loc// /@20} cookie=\$(cat credential.json | grep -A 1 '\\"${source}\\": {' | grep -o '\\"cookie\\": \\".*\\"') cookie=\${cookie:11:-1}