Maxime U Garcia

### Description of feature This would allow for usage of locally build genomes

### Description of feature Currently in Sarek we suppose that the database is build following the format `genome.db`, like `GRCh37.75`, `GRCh38.105`, `GRCh38.99`, and so on... But actually there are lots...

the nf-test is not working, I'll fix all the nf-tests in a separate PR _Originally posted by @maxulysse in https://github.com/nf-core/sarek/pull/1345#discussion_r1420368234_

I think we don't need to patch anymore and it should work now with the latest version. The rebuild conda recipe fixed it. _Originally posted by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/1345#discussion_r1420339658_

[FEATURE] port pytest to nf-test for sarek modules

1

Consider using the automated tool to facilitate this https://nf-co.re/docs/contributing/modules#migrating-from-pytest-to-nf-test ### Is your feature request related to a problem? Please describe - [ ] #5170 - [x] bcftools/concat - [x] bcftools/mpileup...

[FEATURE] port pytest to nf-test for rnavar modules

6

### Is your feature request related to a problem? Please describe - [x] bedtools/merge - [x] bedtools/sort - [ ] cat/fastq - [ ] custom/dumpsoftwareversions - [ ] ensemblvep/vep -...

new module: custom/awk_fai_to_bed

9

### Is there an existing module for this? - [X] I have searched for the existing module ### Is there an open PR for this? - [X] I have searched...

Fix genomeAttribute usage

1

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

### Tests for components from nf-core modules - [x] Merging #1221 should add tests for all nf-core/modules, nf-core/subworkflows and pipeline level tests. (see [comment](https://github.com/nf-core/rnaseq/pull/1221#issuecomment-1976070384)) ### Tests for local components >...