diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf index 70043b72140b62295e9bc48ed242f011785d9bfb..7cfff2c9a18b89f6a6f7f415214d62d53a309e0c 100644 --- a/workflow/rna-seq.nf +++ b/workflow/rna-seq.nf @@ -2000,7 +2000,8 @@ process failExecutionRun { endInfer="Paired End" else endInfer="unknown" - fipipelineError_details=\$(echo \${pipelineError_details}"|Paired End|"\${endMeta}"|"\${endInfer}"|\\n") + fi + pipelineError_details=\$(echo \${pipelineError_details}"|Paired End|"\${endMeta}"|"\${endInfer}"|\\n") fi if ${pipelineError_stranded} then @@ -2014,7 +2015,7 @@ process failExecutionRun { then pipelineError_details=\$(echo \${pipelineError_details}"|Species|${speciesMeta}|${speciesInfer}|\\n") fi - #pipelineError_details=\${pipelineError_details::-2} + 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}) echo LOG: execution run RID marked as error - \${rid} >> ${repRID}.finalizeExecutionRun.log fi