Error when running 'Cecret' for single reads

[erinyoung]

There is an error that was sent to me on twitter that I need to fix.

Turns out that someone actually wanted to run this with single reads. This isn't unreasonable.

The command used :

staphb-wb cecret --reads_type single single --output test --profile singularity

The error:

gzip: seqyclean/104485_R1_001.fastq.gz_clean*fastq: No such file or directory

Which is true, 'cl*n' should be used instead of 'clean'. 🤦‍♀️

And, in all actuality, I should be using -gz with seqyclean.

In addition to this error, I now realize that there's another error parsing filenames that don't match '_S[0-9]+_L[0-9]+'. These are not unreasonable names (like 104485_R1_001.fastq.gz), so I should actually fix this issue.