fastqc task error check
Summary
fastqc task fails if fastqc fails
Steps to reproduce
run on fastq with invalid structure
Observed bug behavior
Missing output file(s) *_fastqc.zip expected by process
Expected behavior
detect error, make a dummy fastqc.zip
Relevant logs and/or screenshots
Potential fixes
in task script, replace
fastqcErrorOut=$(cat fastqc.out | grep -c 'Failed to process file') || fastqcErrorOut=0
with
fastqcErrorOut=$(cat fastqc.out | grep -c 'Failed to process') || fastqcErrorOut=0