A question like this was asked here, but never answered.
I need to pass fastq files as options to a tool that does not accept gzipped inputs. Is there really no option other than to unzip every one of them?
It fails when I pass the gzipped version:
mytool -s sample.fastq.gz -f fastq -o output
I've tried this, out of desperation (obviously doesn't work):
mytool -s <(zcat | sample.fastq.gz) -f fastq -o output
I can't pipe it directly, but is there an easier/more straightforward way than what I settled on below?
zcat sample.fastq.gz > sample.fastq
mytool -s sample.fastq -f fastq -o output
rm sample.fastq
It's slow and seems like a lot of unnecessary hassle for tons of files. I'm not the best at coding and always up for learning new tricks.
Thanks!
