diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf index 929d4645d12dd77a80a223075d78afa5a052813c..6c7b2e5666d36f3ff6e41a448a910f1bd0e43dda 100644 --- a/workflow/rna-seq.nf +++ b/workflow/rna-seq.nf @@ -1978,10 +1978,10 @@ process failExecutionRun { echo LOG: execution run RID marked as error - \${rid} >> ${repRID}.finalizeExecutionRun.log elif [ ${pipelineError} == true ] then - pipelineError_details=\$(echo "**Submitted metadata does not match infered:** ") - #pipelineError_details=\$(echo "**Submitted metadata does not match infered:**\\n ") - #pipelineError_details=\$(echo "|Metadata|Submitted value|Inferred value|\\n ") - #pipelineError_details=\$(echo "|:-:|-:|-:|\\n") + #pipelineError_details=\$(echo "**Submitted metadata does not match infered:** ") + pipelineError_details=\$(echo "**Submitted metadata does not match infered:**\\n ") + pipelineError_details=\$(echo "|Metadata|Submitted value|Inferred value|\\n ") + pipelineError_details=\$(echo "|:-:|-:|-:|\\n") if ${pipelineError_ends} then if [ "${endsMeta}" == "se" ] @@ -2002,25 +2002,25 @@ process failExecutionRun { else endInfer="unknown" fi - pipelineError_details=\$(echo \${pipelineError_details}"Paired_End: submitted value = \\""\${endMeta}"\\" while inferred value = \\""\${endInfer}"\\". ") - #pipelineError_details=\$(echo \${pipelineError_details}"|*Paired_End*|"\${endMeta}"|"\${endsInfer}"|\\n ") + #pipelineError_details=\$(echo \${pipelineError_details}"Paired_End: submitted value = \\""\${endMeta}"\\" while inferred value = \\""\${endInfer}"\\". ") + pipelineError_details=\$(echo \${pipelineError_details}"|*Paired_End*|"\${endMeta}"|"\${endsInfer}"|\\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}|"${strandedInfer}|\\n ") + #pipelineError_details=\$(echo \${pipelineError_details}"Strandedness: submitted value = \\"${strandedMeta}\\" while inferred value = \\"${strandedInfer}\\". ") + pipelineError_details=\$(echo \${pipelineError_details}"|*Strandedness*|${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}|${spikeInfer}|\\n ") + #pipelineError_details=\$(echo \${pipelineError_details}"Used_Spike_Ins: submitted value = \\"${spikeMeta}\\" while inferred value = \\"${spikeInfer}\\". ") + pipelineError_details=\$(echo \${pipelineError_details}"|*Used_Spike_Ins*|${spikeMeta}|${spikeInfer}|\\n ") 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}|"${speciesInfer}|\\n ") + #pipelineError_details=\$(echo \${pipelineError_details}"Species: submitted value = \\"${speciesMeta}\\" while inferred value = \\"${speciesInfer}\\". ") + pipelineError_details=\$(echo \${pipelineError_details}"|*Species*|${speciesMeta}|"${speciesInfer}|\\n ") fi - pipelineError_details=\$(echo "\${pipelineError_details::-1}") + #pipelineError_details=\$(echo "\${pipelineError_details::-1}") 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