diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf index 6d2d57e0a2e64e9cc2f6693f6f68c01395966181..d29490ed33438ad0fb18863b2fac188494f19b84 100644 --- a/workflow/rna-seq.nf +++ b/workflow/rna-seq.nf @@ -2210,7 +2210,7 @@ process failExecutionRun { pipelineError_details=\$(echo \${pipelineError_details}"|Species|${speciesMeta}|${speciesInfer}|\\n") fi pipelineError_details=\${pipelineError_details::-2} - rid=\$(python3 ${script_uploadExecutionRun_failExecutionRun} -r ${repRID} -w \${workflow} -g \${genome} -i ${inputBagRID} -s Error -d "\${pipelineError_details}" -o ${source} -c \${cookie} -u ${executionRunRID}) + rid=\$(python3 ${script_uploadExecutionRun_failExecutionRun} -r ${repRID} -w \${workflow} -g \${genome} -i ${inputBagRID} -s Error -d \"\${pipelineError_details}\" -o ${source} -c \${cookie} -u ${executionRunRID}) echo LOG: execution run RID marked as error - \${rid} >> ${repRID}.failExecutionRun.log fi """