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Commit 4bce8c2c authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
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Fix pre error details format

parent 0a986962
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2 merge requests!58Develop,!56Resolve "Detect error in inferMetadata for tracking"
Pipeline #8838 passed with stages
in 2 minutes and 34 seconds
...@@ -360,15 +360,15 @@ process parseMetadata { ...@@ -360,15 +360,15 @@ process parseMetadata {
if [ "${fastqCount}" -gt "2" ] if [ "${fastqCount}" -gt "2" ]
then then
fastqCountError=true fastqCountError=true
fastqCountError_details="Too many fastqs detected (>2)" fastqCountError_details="**Too many fastqs detected (>2)**"
elif [ "\${endsMeta}" == "se" ] && [ "${fastqCount}" -ne "1" ] elif [ "\${endsMeta}" == "se" ] && [ "${fastqCount}" -ne "1" ]
then then
fastqCountError=true fastqCountError=true
fastqCountError_details="Number of fastqs detected does not match submitted endness" fastqCountError_details="**Number of fastqs detected does not match submitted endness**"
elif [ "\${endsMeta}" == "pe" ] && [ "${fastqCount}" -ne "2" ] elif [ "\${endsMeta}" == "pe" ] && [ "${fastqCount}" -ne "2" ]
then then
fastqCountError=true fastqCountError=true
fastqCountError_details="Number of fastqs detected does not match submitted endness" fastqCountError_details="**Number of fastqs detected does not match submitted endness**"
fi fi
# check read counts match for fastqs # check read counts match for fastqs
...@@ -381,7 +381,7 @@ process parseMetadata { ...@@ -381,7 +381,7 @@ process parseMetadata {
if [ "\${r1Count}" -ne "\${r2Count}" ] if [ "\${r1Count}" -ne "\${r2Count}" ]
then then
fastqReadError=true fastqReadError=true
fastqReadError_details="Number of reads do not match for R1 or R2, there may be a trunkation or mismatch of fastq files" fastqReadError_details="**Number of reads do not match for R1 and R2:** there may be a trunkation or mismatch of fastq files"
fi fi
fi fi
......
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