FastQC fails when fastq file is not in gzip format

[lwratten]

I found this when I tried to run with the --skip_basecalling flag on some data we have
This is due to the symbolic link we create at the start

Are we making it mandatory for the fastq to be gzipped, or will we add a case here so it doesn't break?

[drpatelh]

This should fail more elegantly in the CheckSampleSheet process right?

nanoseq/bin/check_samplesheet.py

Line 80 in 99a8626

if fastq[-9:] != '.fastq.gz' and fastq[-6:] != '.fq.gz':

Shouldnt be able to get to the FastQC process unless there is a bug somewhere. What does you sample sheet look like @lwratten ?

Yes, I think we should insist on the fastq files being zipped. Much more storage friendly.

[drpatelh]

Ok. I found the bug. Basically we arent exiting if the if statement above fails. Ill fix in the next PR.

[drpatelh]

Fixed in #46