Filipe G. Vieira

Actually, having `N`s int he UMIs affect downstream analyses, namely the `GroupReadsByUmi` step: ``` [2020/01/06 14:17:28 | GroupReadsByUmi | Info] Filtered out 65,529,916 reads that contained one or more Ns...

If option 2 is hard then I'd also prefer option 3, but I find a bit confusing having both `N`s and `n`s with different meanings... can we use another character?...

It seems QUAST checks if the binary exist before trying to install them, so I just manually installed all necessary programs in the conda environment. But it would make more...

Can you also add `gridss`? Not sure if QUAST needs other programs, but those three for sure. Thanks!

yes, but when running `delly` through a pipeline, you not always know if the BED file will be empty or not (since `delly` requires the complement). Another way would be...

Hi @tobiasrausch, I see that you just released a new version of `delly`, would it be possible to also have an include BED file option (like, e.g., in `manta` or...

I agree that it would be nice to have as a debug option.

Not quite sure I understand the issue here. I've used all three VEP snakemake wrappers and never encountered the issues you mention. Can you send a minimal example with the...

The wrapper currently uses the URL `ftp://ftp.ensembl.org/pub/{branch}release-{release}/fasta/{species}/{datatype}/{species_cap}.{spec}.{suffix}`. For ensembl genomes, would it be enough to change it to `ftp://ftp.{source}.org/pub/{branch}release-{release}/fasta/{species}/{datatype}/{species_cap}.{spec}.{suffix}`? Can you provide an example snakemake rule for testing?

I believe this has been fixed on #546. Can you double check?