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Commit e1819c40 authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
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Add excape to bracket in echo

parent 8f5efffa
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2 merge requests!65Develop,!64Resolve "samtools sort: couldn't allocate memory for bam_mem"
Pipeline #9055 canceled with stages
in 6 minutes and 57 seconds
...@@ -388,7 +388,7 @@ process parseMetadata { ...@@ -388,7 +388,7 @@ process parseMetadata {
elif [ "${fastqCount}" -eq "0" ] elif [ "${fastqCount}" -eq "0" ]
then then
fastqCountError=true fastqCountError=true
fastqCountError_details="**No valid fastqs detected (may not match .R{12}.fastq.gz convention)**" fastqCountError_details="**No valid fastqs detected \\(may not match .R{12}.fastq.gz convention\\)**"
elif [ "\${endsMeta}" == "se" ] && [ "${fastqCount}" -ne "1" ] elif [ "\${endsMeta}" == "se" ] && [ "${fastqCount}" -ne "1" ]
then then
fastqCountError=true fastqCountError=true
...@@ -2372,8 +2372,8 @@ process failPreExecutionRun_fastqFile { ...@@ -2372,8 +2372,8 @@ process failPreExecutionRun_fastqFile {
script: script:
""" """
hostname > ${repRID}.failPreExecutionRun_fastq.log hostname > ${repRID}.failPreExecutionRun_fastqfile.log
ulimit -a >> ${repRID}.failPreExecutionRun_fastq.log ulimit -a >> ${repRID}.failPreExecutionRun_fastqfile.log
errorDetails="" errorDetails=""
if [ ${fastqFileError} == true ] if [ ${fastqFileError} == true ]
...@@ -2381,11 +2381,11 @@ process failPreExecutionRun_fastqFile { ...@@ -2381,11 +2381,11 @@ process failPreExecutionRun_fastqFile {
errorDetails=\$(echo \$(errorDetails)${fastqFileError_details}"\\n") errorDetails=\$(echo \$(errorDetails)${fastqFileError_details}"\\n")
fi fi
echo LOG: searching for workflow RID - BICF mRNA ${workflow.manifest.version} >> ${repRID}.failPreExecutionRun_fastq.log echo LOG: searching for workflow RID - BICF mRNA ${workflow.manifest.version} >> ${repRID}.failPreExecutionRun_fastqfile.log
workflow=\$(curl -s https://${source}/ermrest/catalog/2/entity/RNASeq:Workflow/Name=BICF%20mRNA%20Replicate/Version=${workflow.manifest.version}) workflow=\$(curl -s https://${source}/ermrest/catalog/2/entity/RNASeq:Workflow/Name=BICF%20mRNA%20Replicate/Version=${workflow.manifest.version})
workflow=\$(echo \${workflow} | grep -o '\\"RID\\":\\".*\\",\\"RCT') workflow=\$(echo \${workflow} | grep -o '\\"RID\\":\\".*\\",\\"RCT')
workflow=\${workflow:7:-6} workflow=\${workflow:7:-6}
echo LOG: workflow RID extracted - \${workflow} >> ${repRID}.failPreExecutionRun_fastq.log echo LOG: workflow RID extracted - \${workflow} >> ${repRID}.failPreExecutionRun_fastqfile.log
if [ "${species}" == "Homo sapiens" ] if [ "${species}" == "Homo sapiens" ]
then then
...@@ -2398,27 +2398,27 @@ process failPreExecutionRun_fastqFile { ...@@ -2398,27 +2398,27 @@ process failPreExecutionRun_fastqFile {
then then
genomeName=\$(echo \${genomeName}-S) genomeName=\$(echo \${genomeName}-S)
fi fi
echo LOG: searching for genome name - \${genomeName} >> ${repRID}.failPreExecutionRun_fastq.log echo LOG: searching for genome name - \${genomeName} >> ${repRID}.failPreExecutionRun_fastqfile.log
genome=\$(curl -s https://${source}/ermrest/catalog/2/entity/RNASeq:Reference_Genome/Name=\${genomeName}) genome=\$(curl -s https://${source}/ermrest/catalog/2/entity/RNASeq:Reference_Genome/Name=\${genomeName})
genome=\$(echo \${genome} | grep -o '\\"RID\\":\\".*\\",\\"RCT') genome=\$(echo \${genome} | grep -o '\\"RID\\":\\".*\\",\\"RCT')
genome=\${genome:7:-6} genome=\${genome:7:-6}
echo LOG: genome RID extracted - \${genome} >> ${repRID}.failPreExecutionRun_fastq.log echo LOG: genome RID extracted - \${genome} >> ${repRID}.failPreExecutionRun_fastqfile.log
cookie=\$(cat credential.json | grep -A 1 '\\"${source}\\": {' | grep -o '\\"cookie\\": \\".*\\"') cookie=\$(cat credential.json | grep -A 1 '\\"${source}\\": {' | grep -o '\\"cookie\\": \\".*\\"')
cookie=\${cookie:11:-1} cookie=\${cookie:11:-1}
exist=\$(curl -s https://${source}/ermrest/catalog/2/entity/RNASeq:Execution_Run/Workflow=\${workflow}/Replicate=${repRID}/Input_Bag=${inputBagRID}) exist=\$(curl -s https://${source}/ermrest/catalog/2/entity/RNASeq:Execution_Run/Workflow=\${workflow}/Replicate=${repRID}/Input_Bag=${inputBagRID})
echo \${exist} >> ${repRID}.failPreExecutionRun_fastq.log echo \${exist} >> ${repRID}.failPreExecutionRun_fastqfile.log
if [ "\${exist}" == "[]" ] if [ "\${exist}" == "[]" ]
then then
rid=\$(python3 ${script_uploadExecutionRun} -r ${repRID} -w \${workflow} -g \${genome} -i ${inputBagRID} -s Error -d "\${errorDetails}" -o ${source} -c \${cookie} -u F) 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_fastq.log echo LOG: execution run RID uploaded - \${rid} >> ${repRID}.failPreExecutionRun_fastqfile.log
else else
rid=\$(echo \${exist} | grep -o '\\"RID\\":\\".*\\",\\"RCT') rid=\$(echo \${exist} | grep -o '\\"RID\\":\\".*\\",\\"RCT')
rid=\${rid:7:-6} rid=\${rid:7:-6}
echo \${rid} >> ${repRID}.failPreExecutionRun_fastq.log echo \${rid} >> ${repRID}.failPreExecutionRun_fastqfile.log
executionRun_rid==\$(python3 ${script_uploadExecutionRun} -r ${repRID} -w \${workflow} -g \${genome} -i ${inputBagRID} -s Error -d "\${errorDetails}" -o ${source} -c \${cookie} -u \${rid}) 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_fastq.log echo LOG: execution run RID updated - \${executionRun_rid} >> ${repRID}.failPreExecutionRun_fastqfile.log
fi fi
dt=`date +%FT%T.%3N%:z` dt=`date +%FT%T.%3N%:z`
......
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