Thiseas C. Lamnidis

This PR adds modules for `trident`: - [x] trident fetch - [ ] trident validate - [ ] trident forge ## PR checklist Closes #XXX - [x] This comment contains...

nf-core modules lint --fix produces mangled output

2

### Description of the bug When I use `nf-core/modules lint --fix` on a module PR, the resulting meta.yml does not successfully lint. The PR where I encountered the issue: https://github.com/nf-core/modules/pull/9360...

DSL2: nf-test conversion `test_full`

3

Closes #1141 ## PR checklist - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should...

Adding ATLAS as a genotyping alternative to create genotype likelihoods. - Are all needed ATLAS subtools available as a module? - How should these tools be stitched together?

`test_full` nf-test conversion

`test_long` nf-test conversion

When nf-core/eager 3.0.0 is released, we should switch to `main` as the active branch, and away from the current `master`.

Conversion of `test_modern` to nf-test

Conversion of `test_shortdna` to nf-test

DSL2: test_nothing profile is broken

1

## Check Documentation I have checked the following places for your error: - [x] [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting) - [x] [nf-core/eager pipeline documentation](https://nf-co.re/nf-core/eager/usage) - nf-core/eager FAQ/troubleshooting can be found [here](https://nf-co.re/eager/usage#troubleshooting-and-faqs) ##...