Mehrdad Jaberi

Thanks for the great work here, I was wondering if `circos.labels()` could read preAllocated tracks from `chordDiagram`. In the example you showed if the `side` is outside, we need to...

Running IQTREE or RAxML separately

2

Hi Orthofinders, This is not an issue but seeking recommendation. I was wondering if anyone has a suggestion how to run gene tree inference by IQTREE/ RAxML separately. I've divided...

How do you bite rowwise?

2

I'm trying to bite() based on start (X7) and end(X8) columns but I cannot figure it out. 

### Description of the bug deeparg 1.0.2 is using an old repository path to download the databases (https://bench.cs.vt.edu/ftp/) which does not exist. deeparg 1.0.4 fetches data correctly from https://zenodo.org/records/8280582/files/deeparg.zip. Singularity...

### Description of the bug A couple of months ago we had a slack thread about how `NFCORE_FUNCSCAN:FUNCSCAN:GUNZIP_PYRODIGAL_FNA` gets confused with meta.id and gz file path if sample names are...

AMPLIFY_PREDICT exits with a ValueError while checking input

1

### Description of the bug AMPLIFY_PREDICT fails on **some** protein sequences. The issue is discussed on slack [here](https://nfcore.slack.com/archives/C02K5GX2W93/p1714681983734489). Two input sequences for which AMPLIFY_PREDICT fails/passes are [available on Slack](https://nfcore.slack.com/archives/C02K5GX2W93/p1714722105261119?thread_ts=1714681983.734489&cid=C02K5GX2W93). Pyrodigal...

### Description of the bug I cannot overwrite some parameters in custom config file: - `read_length` - `qd_filter` - `fs_filter` - `save_reference` For `qd_filter` and `fs_filter` I used float type...

### Description of feature Dear `nf-core/rnavar` authors, It would be an amazing feature to include sorting intolerant from tolerant algorithm in the pipeline and rank which one of the variants...

### Actual Behavior Cannot render and apply node size based on degree with a network containing isolated nodes (degree = 0) ### Expected/Desired Behavior Node size based on degree should...

nucleotide specific fileds are empty while importing AmrFinderPlus results based on nucleotide sequences

2

I have the following results from AmrFinderPlus by passing `--name`. ``` --name NAME Text to be added as the first column "name" to all rows of the report, for example...