Tests fail on bwameth_align_trimmed

[Blosberg]

Current tests with sample_sheet in tests break on bwameth_align_trimmed.

Logfile says

Exception: bad or empty fastqs

Seems reminiscent of this issue, but happening upstream of the samtools view.

[alexg9010]

HI @Blosberg ,

Nice to hear from you, hope you are doing well :)

Could you verify that the pipeline is using the latest versions of bwameth?
Maybe check in the generated config.json that the version is >= 0.2.2, which is the version I used for testing.

Best,
Alex

[Blosberg]

Hi Alex.
All is well 👍

$bwa-meth.py --version
returns:
bwa-meth.py 0.2.2

I noticed that the shortened fasta reference has been removed from the repo at /tests/genome/ --are tests now aligning against the full hg19 (somewhere outside of /tests/)?

[alexg9010]

Oh, I forgot to add the sample.fasta to the repo.

I'll fix that.

[Blosberg]

Hi Alex.
Thanks for adding sample.fasta to the repo.
I'm fine with the name (so ignore the other comment), but the error that is encountered on rule bwameth_align_trimmed is unchanged:
command exits with non-zero status
The bottom of the bwameth_mapping.log file reads Exception: bad or empty fastqs. The corresponding files are not empty in 02_trimming, but perhaps there are simply zero alignments?