diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf index 70c96da623e4118d7b6e78d65530a61462f72133..5f13a4ee25c4aa8cc4c9fba1acf26b4a7df19eb2 100644 --- a/workflow/rna-seq.nf +++ b/workflow/rna-seq.nf @@ -2000,21 +2000,21 @@ process failExecutionRun { endInfer="Paired End" else endInfer="unknown" - fipipelineError_details=\$(echo \${pipelineError_details}"|*Paired End*|"\${endMeta}"|"\${endInfer}"|\\n") + fipipelineError_details=\$(echo \${pipelineError_details}"|Paired End|"\${endMeta}"|"\${endInfer}"|\\n") fi if ${pipelineError_stranded} - then#pipelineError_details=\$(echo \${pipelineError_details}"Strandedness: submitted value = \\"${strandedMeta}\\" while inferred value = \\"${strandedInfer}\\". ") - pipelineError_details=\$(echo \${pipelineError_details}"|*Strandedness*|${strandedMeta}|${strandedInfer}|\\n") + then + pipelineError_details=\$(echo \${pipelineError_details}"|Strandedness|${strandedMeta}|${strandedInfer}|\\n") fi if ${pipelineError_spike} - then#pipelineError_details=\$(echo \${pipelineError_details}"Used_Spike_Ins: submitted value = \\"${spikeMeta}\\" while inferred value = \\"${spikeInfer}\\". ") - pipelineError_details=\$(echo \${pipelineError_details}"|*Used Spike Ins*|${spikeMeta}|${spikeInfer}|\\n") + then + pipelineError_details=\$(echo \${pipelineError_details}"|Used Spike Ins|${spikeMeta}|${spikeInfer}|\\n") fi if ${pipelineError_species} - then#pipelineError_details=\$(echo \${pipelineError_details}"Species: submitted value = \\"${speciesMeta}\\" while inferred value = \\"${speciesInfer}\\". ") - pipelineError_details=\$(echo \${pipelineError_details}"|*Species*|${speciesMeta}|${speciesInfer}|\\n") + then + pipelineError_details=\$(echo \${pipelineError_details}"|Species|${speciesMeta}|${speciesInfer}|\\n") fi - pipelineError_details=\$(echo "\${pipelineError_details::-2}") + #ipelineError_details=\$(echo "\${pipelineError_details::-}") 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