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Commit 985cef31 authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
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Fix fastqc error detection

parent c36fec03
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2 merge requests!65Develop,!64Resolve "samtools sort: couldn't allocate memory for bam_mem"
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workflow/rna-seq.nf
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...@@ -570,12 +570,11 @@ process fastqc { ...@@ -570,12 +570,11 @@ process fastqc {
# run fastqc # run fastqc
echo -e "LOG: running fastq on raw fastqs" >> ${repRID}.fastqc.log echo -e "LOG: running fastq on raw fastqs" >> ${repRID}.fastqc.log
fastqcErrorOut=false fastqcErrorOut=0
fastqc *.fastq.gz -o . &> fastqc.out || : fastqc *.fastq.gz -o . &> fastqc.out || fastqcErrorOut=\$(cat fastqc.out | grep -c 'Failed to process file')
fastqcErrorOut=\$(cat fastqc.out | grep -c 'Failed to process file')
fastqFileError=false fastqFileError=false
fastqFileError_details="" fastqFileError_details=""
if [ "\${fastqcErrorOut}" -gt "0" ] if [ "\${fastqcErrorOut}" -ne "0" ]
then then
fastqFileError=true fastqFileError=true
fastqFileError_details="**There is an error with the structure of the fastq**" fastqFileError_details="**There is an error with the structure of the fastq**"
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