Error when the files containing the genome assembly and the reads share the same basename

[jesvedberg]

If you have given both the file containing the draft genome assembly and reads the same basename (for instance mysample.fa and mysample.fq.gz), tigmint will run, but not generate any cuts. Note: I've only tested this in the tigmint-long mode.

As far as I can tell, the reason for this appears to be that the make pipline will think that the mysample.fa file contains reads, and it will use that file instead of mysample.fq.gz.

You can easily work around this problem by renaming one of the files, but it took me a couple of hours to figure out (especially since it doesn't actually produce an error), so it would probably be a good idea to at the very least mention this limitation in documentation.

[warrenlr]

noted. thank you for your report @jesvedberg