diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf index a9d3aa70a477176e18b497b49d24d36e99948b28..64a5d1bbff5f557947de28470d7b50aab8297fdb 100644 --- a/workflow/rna-seq.nf +++ b/workflow/rna-seq.nf @@ -1979,12 +1979,16 @@ process failExecutionRun { 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") if ${pipelineError_ends} then if [ "${endsMeta}" == "se" ] then endMeta="Single End" elif [ "${endsMeta}" == "pe" ] + then endMeta="Paired End" else endMeta="unknown" @@ -1998,18 +2002,22 @@ process failExecutionRun { endInfer="unknown" fi pipelineError_details=\$(echo \${pipelineError_details}"Paired_End: submitted value = \""\${endMeta}"\" while inferred value = \""\${endsInfer}"\". ") + #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 ") 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 ") fi if ${pipelineError_species} then - pipelineError_details=\$(echo \${pipelineError_details}"[ Species: submitted value = \"${speciesMeta}\" while inferred value = \"${speciesInfer}\". ") + pipelineError_details=\$(echo \${pipelineError_details}"Species: submitted value = \"${speciesMeta}\" while inferred value = \"${speciesInfer}\". ") + #pipelineError_details=\$(echo \${pipelineError_details}"|*Species*|${speciesMeta}|"${speciesInfer}|\n ") fi pipelineError_details=\$(echo "\${pipelineError_details::-1}" rid=\$(python3 ${script_uploadExecutionRun_failExecutionRun} -r ${repRID} -w \${workflow} -g \${genome} -i ${inputBagRID} -s Error -d "\${pipelineError_details}" -o ${source} -c \${cookie} -u ${executionRunRID})