João Cavalcante

- **nf-test: Migrate phispy tests** - **chore: Remove pytest test for phispy** ## PR checklist Closes #5261 - [x] This comment contains a description of changes (with reason). - [x]...

### Is your feature request related to a problem? Please describe pytest -> nf-test migration for [PhiSpy](https://nf-co.re/modules/phispy) ### Describe the solution you'd like _No response_ ### Describe alternatives you've considered...

Mob_Recon fails with compressed input

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Hi, I'm using mob_recon (v3.1.7) on some assemblies and I've noticed that it fails when using a gzip-compressed file and succeeds when using the same file, but decompressed. It looks...

MAFFT error when running ppanggolin MSA

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- PPanGGOLIN v2.0.5 Hi, after running and creating the pangenome file with this command, for about ~1600 GFFs: ```sh ppanggolin \ workflow \ --cpu 24 \ --anno ppanggolin_samplesheet.tsv \ --output...

Currently, the tests are slow to run and could use some improvements, such as being more self-contained and less reliant on external data services, to account for situations such as...

Expose the data extension service through reconciler. [Spec](https://reconciliation-api.github.io/specs/latest/#data-extension-service) Idea by @gitonthescene on #11

The new API version (v2), [allows for pagination](https://clinicaltrials.gov/data-api/api#get-/studies), support this.

[For future reference](https://github.com/beiko-lab/Indizio) - Add documentation for running Indizio on ARETE outputs

Subworkflow install failure still results in a 0 exit code

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### Description of the bug When installing a subworkflow, if tools can't find a module within this subworkflow it raises an error message, but the error code returned at the...

feat: Install subworkflows with modules from different remotes

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## PR checklist - [x] This comment contains a description of changes (with reason) - [ ] `CHANGELOG.md` is updated - [x] If you've fixed a bug or added code...