andreott

metaphlan2krona.py not working

1

Hi, metaphlan2krona.py fails as it does not expect the additional species field. For me I used the trivial fix locally by adding line 37 ```python aline = '\t'.join(aline.split('\t')[:-1]) ``` https://github.com/biobakery/MetaPhlAn/blob/46ef712a590faca541e9fa293eda891216d39994/metaphlan/utils/metaphlan2krona.py#L35-L42

Hi! it would be great to have an option to set the zero coverage symbol at execution to easily distinguish between uncovered regions and genuine deletions. Of course, we can...

STAR index wrapper with GFF

1

**Is your feature request related to a problem? Please describe.** When using STAR index with a GFF instead of GTF file, the flag `--sjdbGTFtagExonParentTranscript Parent` needs to be passed. **Describe...

Hisat2 align on large index

6

**Snakemake version** *snakemake-wrappers:* 3.3.3 **Describe the bug** The wrapper looks for the index file checking for *.ht2* file extension only. So this fails when a *large* index was produced with...

No matter how high I set the -z value, there are no stars. Removing the backslash in the line below fixes the problem for me. https://github.com/jordanlab/stringMLST/blob/84e74334783321c463d93d2cc11648cc8a1df2d3/stringMLST.py#L604