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Commit e5783b29 authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
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Add new fail pre ex run for seqwho

parent aaac13e4
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1 merge request!87Develop
Pipeline #9921 passed with warnings with stages
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with 113 additions and 10 deletions
rna-seq.nf
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− 10
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...@@ -51,6 +51,7 @@ deriva.into { ...@@ -51,6 +51,7 @@ deriva.into {
deriva_uploadOutputBag deriva_uploadOutputBag
deriva_finalizeExecutionRun deriva_finalizeExecutionRun
deriva_failPreExecutionRun deriva_failPreExecutionRun
deriva_failPreExecutionRun_seqwho
deriva_failExecutionRun deriva_failExecutionRun
} }
bdbag = Channel bdbag = Channel
...@@ -105,6 +106,7 @@ script_uploadInputBag = Channel.fromPath("${baseDir}/workflow/scripts/upload_inp ...@@ -105,6 +106,7 @@ script_uploadInputBag = Channel.fromPath("${baseDir}/workflow/scripts/upload_inp
script_uploadExecutionRun_uploadExecutionRun = Channel.fromPath("${baseDir}/workflow/scripts/upload_execution_run.py") script_uploadExecutionRun_uploadExecutionRun = Channel.fromPath("${baseDir}/workflow/scripts/upload_execution_run.py")
script_uploadExecutionRun_finalizeExecutionRun = Channel.fromPath("${baseDir}/workflow/scripts/upload_execution_run.py") script_uploadExecutionRun_finalizeExecutionRun = Channel.fromPath("${baseDir}/workflow/scripts/upload_execution_run.py")
script_uploadExecutionRun_failPreExecutionRun = Channel.fromPath("${baseDir}/workflow/scripts/upload_execution_run.py") script_uploadExecutionRun_failPreExecutionRun = Channel.fromPath("${baseDir}/workflow/scripts/upload_execution_run.py")
script_uploadExecutionRun_failPreExecutionRun_seqwho = Channel.fromPath("${baseDir}/workflow/scripts/upload_execution_run.py")
script_uploadExecutionRun_failExecutionRun = Channel.fromPath("${baseDir}/workflow/scripts/upload_execution_run.py") script_uploadExecutionRun_failExecutionRun = Channel.fromPath("${baseDir}/workflow/scripts/upload_execution_run.py")
script_uploadQC = Channel.fromPath("${baseDir}/workflow/scripts/upload_qc.py") script_uploadQC = Channel.fromPath("${baseDir}/workflow/scripts/upload_qc.py")
script_uploadQC_fail = Channel.fromPath("${baseDir}/workflow/scripts/upload_qc.py") script_uploadQC_fail = Channel.fromPath("${baseDir}/workflow/scripts/upload_qc.py")
...@@ -523,6 +525,7 @@ spikeMeta.into { ...@@ -523,6 +525,7 @@ spikeMeta.into {
spikeMeta_aggrQC spikeMeta_aggrQC
spikeMeta_uploadExecutionRun spikeMeta_uploadExecutionRun
spikeMeta_failPreExecutionRun spikeMeta_failPreExecutionRun
spikeMeta_failPreExecutionRun_seqwho
spikeMeta_failExecutionRun spikeMeta_failExecutionRun
} }
speciesMeta.into { speciesMeta.into {
...@@ -530,6 +533,7 @@ speciesMeta.into { ...@@ -530,6 +533,7 @@ speciesMeta.into {
speciesMeta_checkMetadata speciesMeta_checkMetadata
speciesMeta_aggrQC speciesMeta_aggrQC
speciesMeta_failPreExecutionRun speciesMeta_failPreExecutionRun
speciesMeta_failPreExecutionRun_seqwho
speciesMeta_failExecutionRun speciesMeta_failExecutionRun
} }
studyRID.into { studyRID.into {
...@@ -954,7 +958,7 @@ speciesInfer.into { ...@@ -954,7 +958,7 @@ speciesInfer.into {
speciesInfer_aggrQC speciesInfer_aggrQC
speciesInfer_uploadExecutionRun speciesInfer_uploadExecutionRun
speciesInfer_uploadProcessedFile speciesInfer_uploadProcessedFile
speciesInfer_failPreExecutionRun speciesInfer_failPreExecutionRun_seqwho
speciesInfer_failExecutionRun speciesInfer_failExecutionRun
} }
...@@ -2257,6 +2261,7 @@ inputBagRID.into { ...@@ -2257,6 +2261,7 @@ inputBagRID.into {
inputBagRID_uploadExecutionRun inputBagRID_uploadExecutionRun
inputBagRID_finalizeExecutionRun inputBagRID_finalizeExecutionRun
inputBagRID_failPreExecutionRun inputBagRID_failPreExecutionRun
inputBagRID_failPreExecutionRun_seqwho
inputBagRID_failExecutionRun inputBagRID_failExecutionRun
} }
...@@ -2681,11 +2686,17 @@ process finalizeExecutionRun { ...@@ -2681,11 +2686,17 @@ process finalizeExecutionRun {
// Combine errors // Combine errors
error_meta = fastqCountError_uploadQC_fail.ifEmpty(false).combine(fastqReadError_uploadQC_fail.ifEmpty(false).combine(fastqFileError_uploadQC_fail.ifEmpty(false).combine(seqtypeError_uploadQC_fail.ifEmpty(false).combine(speciesErrorSeqwho_uploadQC_fail.ifEmpty(false).combine(speciesError_uploadQC_fail.ifEmpty(false).combine(pipelineError_uploadQC_fail.ifEmpty(false))))))) error_meta = fastqCountError_uploadQC_fail.ifEmpty(false).combine(fastqReadError_uploadQC_fail.ifEmpty(false).combine(fastqFileError_uploadQC_fail.ifEmpty(false).combine(seqtypeError_uploadQC_fail.ifEmpty(false).combine(speciesErrorSeqwho_uploadQC_fail.ifEmpty(false).combine(speciesError_uploadQC_fail.ifEmpty(false).combine(pipelineError_uploadQC_fail.ifEmpty(false)))))))
error_meta. into { error_meta.into {
error_failPreExecutionRun error_failPreExecutionRun
error_failPreExecutionRun_seqwho
error_uploadQC_fail error_uploadQC_fail
} }
errorDetails = fastqCountError_details.ifEmpty("").combine(fastqReadError_details.ifEmpty("").combine(fastqFileError_details.ifEmpty("").combine(seqtypeError_details.ifEmpty("").combine(speciesErrorSeqwho_details.ifEmpty(""))))) errorDetails = fastqCountError_details.ifEmpty("").combine(fastqReadError_details.ifEmpty("").combine(fastqFileError_details.ifEmpty("").combine(seqtypeError_details.ifEmpty("").combine(speciesErrorSeqwho_details.ifEmpty("")))))
errorDetails.into {
errorDetails_failPreExecutionRun
errorDetails_failPreExecutionRun_seqwho
}
/* /*
* failPreExecutionRun: fail the execution run prematurely for fastq errors * failPreExecutionRun: fail the execution run prematurely for fastq errors
...@@ -2698,17 +2709,16 @@ process failPreExecutionRun { ...@@ -2698,17 +2709,16 @@ process 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 speciesMeta 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 (speciesErrorSeqwho_details) from errorDetails tuple val (fastqCountError_details), val (fastqReadError_details), val (fastqFileError_details), val (seqtypeError_details), val (speciesErrorSeqwho_details) from errorDetails_failPreExecutionRun
output: output:
path ("executionRunRID.csv") into executionRunRID_preFail_fl path ("executionRunRID.csv") into executionRunRID_preFail_fl
when: when:
upload upload
fastqCountError == "true" || fastqReadError == "true" || fastqFileError == "true" || seqtypeError == "true" || speciesError == "true" fastqCountError == "true" || fastqReadError == "true" || fastqFileError == "true"
script: script:
""" """
...@@ -2725,7 +2735,99 @@ process failPreExecutionRun { ...@@ -2725,7 +2735,99 @@ process failPreExecutionRun {
elif [ ${fastqFileError} == true ] elif [ ${fastqFileError} == true ]
then then
errorDetails=\$(echo "\${errorDetails}${fastqFileError_details}\\n") errorDetails=\$(echo "\${errorDetails}${fastqFileError_details}\\n")
elif [ ${seqtypeError} == true ] fi
echo LOG: searching for workflow RID - BICF mRNA ${workflow.manifest.version} >> ${repRID}.failPreExecutionRun.log
workflow=\$(curl -s https://${source}/ermrest/catalog/2/entity/RNASeq:Workflow/Name=BICF%20mRNA%20Replicate/Version=${workflow.manifest.version})
workflow=\$(echo \${workflow} | grep -o '\\"RID\\":\\".*\\",\\"RCT')
workflow=\${workflow:7:-6}
echo LOG: workflow RID extracted - \${workflow} >> ${repRID}.failPreExecutionRun.log
if [ "${speciesMeta}" == "Homo sapiens" ]
then
genomeName=\$(echo GRCh${refHuVersion})
elif [ "${speciesMeta}" == "Mus musculus" ]
then
genomeName=\$(echo GRCm${refMoVersion})
fi
if [ "${spike}" == "true" ]
then
genomeName=\$(echo \${genomeName}-S)
fi
echo LOG: searching for genome name - \${genomeName} >> ${repRID}.failPreExecutionRun.log
genome=\$(curl -s https://${source}/ermrest/catalog/2/entity/RNASeq:Reference_Genome/Name=\${genomeName})
genome=\$(echo \${genome} | grep -o '\\"RID\\":\\".*\\",\\"RCT')
genome=\${genome:7:-6}
echo LOG: genome RID extracted - \${genome} >> ${repRID}.failPreExecutionRun.log
cookie=\$(cat credential.json | grep -A 1 '\\"${source}\\": {' | grep -o '\\"cookie\\": \\".*\\"')
cookie=\${cookie:11:-1}
exist=\$(curl -s https://${source}/ermrest/catalog/2/entity/RNASeq:Execution_Run/Workflow=\${workflow}/Replicate=${repRID}/Input_Bag=${inputBagRID})
echo \${exist} >> ${repRID}.failPreExecutionRun.log
if [ "\${exist}" == "[]" ]
then
rid=\$(python3 ${script_uploadExecutionRun} -r ${repRID} -w \${workflow} -g \${genome} -i ${inputBagRID} -s Error -d "\${errorDetails}" -o ${source} -c \${cookie} -u F)
echo LOG: execution run RID uploaded - \${rid} >> ${repRID}.failPreExecutionRun.log
else
rid=\$(echo \${exist} | grep -o '\\"RID\\":\\".*\\",\\"RCT')
rid=\${rid:7:-6}
echo \${rid} >> ${repRID}.failPreExecutionRun.log
executionRun_rid=\$(python3 ${script_uploadExecutionRun} -r ${repRID} -w \${workflow} -g \${genome} -i ${inputBagRID} -s Error -d "\${errorDetails}" -o ${source} -c \${cookie} -u \${rid})
echo LOG: execution run RID updated - \${executionRun_rid} >> ${repRID}.failPreExecutionRun.log
fi
echo "\${rid}" > executionRunRID.csv
if [ ${params.track} == true ]
then
dt=`date +%FT%T.%3N%:z`
curl -H 'Content-Type: application/json' -X PUT -d \
'{ \
"ID": "${workflow.sessionId}", \
"ExecutionRunRID": "'\${rid}'", \
"Failure": "'\${dt}'" \
}' \
"https://9ouc12dkwb.execute-api.us-east-2.amazonaws.com/prod/db/track"
fi
"""
}
// Extract execution run RID into channel
executionRunRID_preFail = Channel.create()
executionRunRID_preFail_fl.splitCsv(sep: ",", header: false).separate(
executionRunRID_preFail
)
/*
* failPreExecutionRun_seqwho: fail the execution run prematurely for seqwho errors
*/
process failPreExecutionRun_seqwho {
tag "${repRID}"
input:
path script_uploadExecutionRun from script_uploadExecutionRun_failPreExecutionRun_seqwho
path credential, stageAs: "credential.json" from deriva_failPreExecutionRun_seqwho
val spike from spikeMeta_failPreExecutionRun_seqwho
val speciesMeta from speciesMeta_failPreExecutionRun_seqwho
val speciesInfer from speciesInfer_failPreExecutionRun_seqwho
val inputBagRID from inputBagRID_failPreExecutionRun_seqwho
tuple val (fastqCountError), val (fastqReadError), val (fastqFileError), val (seqtypeError), val (speciesErrorSeqwho), val (speciesError), val (pipelineError) from error_failPreExecutionRun_seqwho
tuple val (fastqCountError_details), val (fastqReadError_details), val (fastqFileError_details), val (seqtypeError_details), val (speciesErrorSeqwho_details) from errorDetails_failPreExecutionRun_seqwho
output:
path ("executionRunRID.csv") into executionRunRID_preFailseqwho_fl
when:
upload
seqtypeError == "true" || speciesError == "true"
script:
"""
hostname > ${repRID}.failPreExecutionRun.log
ulimit -a >> ${repRID}.failPreExecutionRun.log
errorDetails=""
if [ ${seqtypeError} == true ]
then then
errorDetails=\$(echo "\${errorDetails}${seqtypeError_details}\\n") errorDetails=\$(echo "\${errorDetails}${seqtypeError_details}\\n")
elif [ ${speciesError} == true ] elif [ ${speciesError} == true ]
...@@ -2792,12 +2894,13 @@ process failPreExecutionRun { ...@@ -2792,12 +2894,13 @@ process failPreExecutionRun {
""" """
} }
// Extract execution run RID into channel // Extract execution run RID into channel
executionRunRID_preFail = Channel.create() executionRunRID_preFailseqwho = Channel.create()
executionRunRID_preFail_fl.splitCsv(sep: ",", header: false).separate( executionRunRID_preFailseqwho_fl.splitCsv(sep: ",", header: false).separate(
executionRunRID_preFail executionRunRID_preFailseqwho
) )
failExecutionRunRID = executionRunRID_fail.ifEmpty('').mix(executionRunRID_preFail.ifEmpty('')).filter { it != "" }
failExecutionRunRID = executionRunRID_fail.ifEmpty('').mix(executionRunRID_preFail.ifEmpty('').mix(executionRunRID_preFailseqwho.ifEmpty('')).filter { it != "" }
/* /*
* failExecutionRun: fail the execution run * failExecutionRun: fail the execution run
......
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