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Commit f9f3d1ea authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
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Fix seqwho errors

parent c0e6c659
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1 merge request!85Fix seqwho errors
Pipeline #9796 passed with stages
in 3 minutes and 44 seconds
...@@ -896,7 +896,7 @@ process seqwho { ...@@ -896,7 +896,7 @@ process seqwho {
if [ \${consensus} == false ] if [ \${consensus} == false ]
then then
seqtypeError=true 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}"|fastq|Infered seq type|Infered seq type confidence|\\n")
seqtypeError_details=\$(echo \${seqtypeError_details}"|:--|:--:|:--:|\\n") seqtypeError_details=\$(echo \${seqtypeError_details}"|:--|:--:|:--:|\\n")
seqtypeError_details=\$(echo \${seqtypeError_details}"|Read 1|\${seqtypeR1}|\${seqtypeConfidenceR1}|\\n") seqtypeError_details=\$(echo \${seqtypeError_details}"|Read 1|\${seqtypeR1}|\${seqtypeConfidenceR1}|\\n")
...@@ -952,6 +952,7 @@ speciesInfer.into { ...@@ -952,6 +952,7 @@ speciesInfer.into {
speciesInfer_aggrQC speciesInfer_aggrQC
speciesInfer_uploadExecutionRun speciesInfer_uploadExecutionRun
speciesInfer_uploadProcessedFile speciesInfer_uploadProcessedFile
speciesInfer_failPreExecutionRun
speciesInfer_failExecutionRun speciesInfer_failExecutionRun
} }
...@@ -2695,10 +2696,11 @@ process failPreExecutionRun { ...@@ -2695,10 +2696,11 @@ process failPreExecutionRun {
path script_uploadExecutionRun from script_uploadExecutionRun_failPreExecutionRun path script_uploadExecutionRun from script_uploadExecutionRun_failPreExecutionRun
path credential, stageAs: "credential.json" from deriva_failPreExecutionRun path credential, stageAs: "credential.json" from deriva_failPreExecutionRun
val spike from spikeMeta_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 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), 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: output:
path ("executionRunRID.csv") into executionRunRID_preFail_fl path ("executionRunRID.csv") into executionRunRID_preFail_fl
...@@ -2715,7 +2717,7 @@ process failPreExecutionRun { ...@@ -2715,7 +2717,7 @@ process failPreExecutionRun {
errorDetails="" errorDetails=""
if [ ${fastqCountError} == true ] if [ ${fastqCountError} == true ]
then then
errorDetails=\$(echo "${fastqCountError_details}"\\n") errorDetails=\$(echo "${fastqCountError_details}\\n")
elif [ ${fastqReadError} == true ] elif [ ${fastqReadError} == true ]
then then
errorDetails=\$(echo "\${errorDetails}${fastqReadError_details}\\n") errorDetails=\$(echo "\${errorDetails}${fastqReadError_details}\\n")
...@@ -2727,7 +2729,10 @@ process failPreExecutionRun { ...@@ -2727,7 +2729,10 @@ process failPreExecutionRun {
errorDetails=\$(echo "\${errorDetails}${seqtypeError_details}\\n") errorDetails=\$(echo "\${errorDetails}${seqtypeError_details}\\n")
elif [ ${speciesError} == true ] elif [ ${speciesError} == true ]
then then
errorDetails=\$(echo "\${errorDetails}${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 fi
echo LOG: searching for workflow RID - BICF mRNA ${workflow.manifest.version} >> ${repRID}.failPreExecutionRun.log echo LOG: searching for workflow RID - BICF mRNA ${workflow.manifest.version} >> ${repRID}.failPreExecutionRun.log
...@@ -2736,10 +2741,10 @@ process failPreExecutionRun { ...@@ -2736,10 +2741,10 @@ process failPreExecutionRun {
workflow=\${workflow:7:-6} workflow=\${workflow:7:-6}
echo LOG: workflow RID extracted - \${workflow} >> ${repRID}.failPreExecutionRun.log echo LOG: workflow RID extracted - \${workflow} >> ${repRID}.failPreExecutionRun.log
if [ "${species}" == "Homo sapiens" ] if [ "${speciesMeta}" == "Homo sapiens" ]
then then
genomeName=\$(echo GRCh${refHuVersion}) genomeName=\$(echo GRCh${refHuVersion})
elif [ "${species}" == "Mus musculus" ] elif [ "${speciesMeta}" == "Mus musculus" ]
then then
genomeName=\$(echo GRCm${refMoVersion}) genomeName=\$(echo GRCm${refMoVersion})
fi fi
......
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