Sofia Stamouli

Add alternative long-read (nanopore) preprocessing tools

17

### Description of feature Since Porechop is no longer supported, it is maybe useful to investigate [Porechop_ABI](https://github.com/bonsai-team/Porechop_ABI) as alternative. Or https://github.com/epi2me-labs/pychopper

### Description of feature https://github.com/esteinig/nanoq Ultra-fast quality control and summary reports for nanopore reads

### Description of feature Once all the tools are implemented in taxprofiler, we should do an optimization of the resource settings.

Profiling of long-reads with mOTUs

3

### Description of feature Since mOTUs 3.0.3 it is possible to profile long reads with mOTUs.

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.

Add metamaps/classify

3

## PR checklist Closes the secode module for #1403 - [x] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added...

Add prefix to output file for barrnap

2

## PR checklist Updates barrnap module to include prefix in the output filename. - [ ] This comment contains a description of changes (with reason). - [ ] If you've...

This PR updates the `hasta.config` for taxprofiler Please follow these steps before submitting your PR: - [ ] If your PR is a work in progress, include `[WIP]` in its...

Add MetaMaps classifier

4

Closes #70 ## PR checklist - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should...

Update documentation to include db_type

2

This PR updates the documentation to describe the `db_type` column that has been added in database samplesheet. ## PR checklist - [x] This comment contains a description of changes (with...