taxpasta

taxpasta copied to clipboard

[Feature] Adding metabarcoding/amplicon support

1

### Checklist - [X] There are [no similar issues or pull requests](https://github.com/taxprofiler/taxpasta/issues) for this yet. ### Problem A simmilar issue of different file formats exists for amplicon analysis tools, such...

paulzierep

[Feature] add an option to let taxpasta report relative abundance as fractions instead of only counts

1

### Is there an existing issue for this? - [X] I have searched the existing issues ### Problem description See [discussion on Slack](https://nfcore.slack.com/archives/C031QH57DSS/p1701903800138819) reported by @AmaliT. The following config causes...

Midnighter

[Feature] Changing/adding taxonomies on standardized profile tables

1

### Checklist - [X] There are [no similar issues or pull requests](https://github.com/taxprofiler/taxpasta/issues) for this yet. ### Problem Currently taxpasta can add taxonomic names when standardizing profiler output. Sometimes a table...

Swindle98

[BUG] MetaPhlAn 4 output with duplicate clade tax id is not supported

4

### Is there an existing issue for this? - [X] I have searched the existing issues ### Problem description As in title, this report is forward from https://github.com/nf-core/taxprofiler/issues/396. The MetaPhlAn...

MajoroMask

Should we support the OPAL format as output?

9

In order to use the [OPAL tool](https://github.com/CAMI-challenge/OPAL) for analysis and visualization, it might be useful to convert any supported profiler to [that format](https://github.com/bioboxes/rfc/tree/master/data-format).

Midnighter

[Feature] Allow to set threshold for compositionality check of Bracken results

12

### Checklist - [X] There are [no similar issues or pull requests](https://github.com/taxprofiler/taxpasta/issues) for this yet. ### Problem I would like to merge multiple Bracken output tables. Prior to merging them,...

alexhbnr

Midnighter

I think sourmash is an interesting tool, as it is so fast in scanning vast libraries of genomes. We should add support for its output.

Midnighter

We are in full control of the creation of domain models, hence, we should not allow domain models to coerce their input types. This increases overall type strictness.

Midnighter

From a comment in mOTUs PR so we do not forget: Apparently, mOTUs profiles can contain duplicate tax IDs. Clarify with Sofia and Maxime. For now, sum up read counts.

sofstam