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Commit f9f3d1ea authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
Browse files

Fix seqwho errors

parent c0e6c659
1 merge request!85Fix seqwho errors
Pipeline #9796 passed with stages
in 3 minutes and 44 seconds
......@@ -896,7 +896,7 @@ process seqwho {
if [ \${consensus} == false ]
then
seqtypeError=true
seqtypeError_details=\$(echo "**Infered species confidence is low:**\\n")
seqtypeError_details=\$(echo "**Infered sequence-type confidence is low:**\\n")
seqtypeError_details=\$(echo \${seqtypeError_details}"|fastq|Infered seq type|Infered seq type confidence|\\n")
seqtypeError_details=\$(echo \${seqtypeError_details}"|:--|:--:|:--:|\\n")
seqtypeError_details=\$(echo \${seqtypeError_details}"|Read 1|\${seqtypeR1}|\${seqtypeConfidenceR1}|\\n")
......@@ -952,6 +952,7 @@ speciesInfer.into {
speciesInfer_aggrQC
speciesInfer_uploadExecutionRun
speciesInfer_uploadProcessedFile
speciesInfer_failPreExecutionRun
speciesInfer_failExecutionRun
}
......@@ -2695,10 +2696,11 @@ process failPreExecutionRun {
path script_uploadExecutionRun from script_uploadExecutionRun_failPreExecutionRun
path credential, stageAs: "credential.json" from deriva_failPreExecutionRun
val spike from spikeMeta_failPreExecutionRun
val species from speciesMeta_failPreExecutionRun
val speciesMeta from speciesMeta_failPreExecutionRun
val speciesInfer from speciesInfer_failPreExecutionRun
val inputBagRID from inputBagRID_failPreExecutionRun
tuple val (fastqCountError), val (fastqReadError), val (fastqFileError), val (seqtypeError), val (speciesErrorSeqwho), val (speciesError), val (pipelineError) from error_failPreExecutionRun
tuple val (fastqCountError_details), val (fastqReadError_details), val (fastqFileError_details), val (seqtypeError_details), val (speciesError_details) from errorDetails
tuple val (fastqCountError_details), val (fastqReadError_details), val (fastqFileError_details), val (seqtypeError_details), val (speciesErrorSeqwho_details) from errorDetails
output:
path ("executionRunRID.csv") into executionRunRID_preFail_fl
......@@ -2715,7 +2717,7 @@ process failPreExecutionRun {
errorDetails=""
if [ ${fastqCountError} == true ]
then
errorDetails=\$(echo "${fastqCountError_details}"\\n")
errorDetails=\$(echo "${fastqCountError_details}\\n")
elif [ ${fastqReadError} == true ]
then
errorDetails=\$(echo "\${errorDetails}${fastqReadError_details}\\n")
......@@ -2727,7 +2729,10 @@ process failPreExecutionRun {
errorDetails=\$(echo "\${errorDetails}${seqtypeError_details}\\n")
elif [ ${speciesError} == true ]
then
errorDetails=\$(echo "\${errorDetails}${speciesError_details}\\n")
errorDetails=\$(echo "\${errorDetails}**Submitted metadata does not match inferred:**\\n")
errorDetails=\$(echo "\${errorDetails}|Metadata|Submitted value|Inferred value|\\n")
errorDetails=\$(echo "\${errorDetails}|:-:|-:|-:|\\n")
errorDetails=\$(echo "\${errorDetails}|Species|${speciesMeta}|${speciesInfer}|\\n")
fi
echo LOG: searching for workflow RID - BICF mRNA ${workflow.manifest.version} >> ${repRID}.failPreExecutionRun.log
......@@ -2736,10 +2741,10 @@ process failPreExecutionRun {
workflow=\${workflow:7:-6}
echo LOG: workflow RID extracted - \${workflow} >> ${repRID}.failPreExecutionRun.log
if [ "${species}" == "Homo sapiens" ]
if [ "${speciesMeta}" == "Homo sapiens" ]
then
genomeName=\$(echo GRCh${refHuVersion})
elif [ "${species}" == "Mus musculus" ]
elif [ "${speciesMeta}" == "Mus musculus" ]
then
genomeName=\$(echo GRCm${refMoVersion})
fi
......
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