Feat/workflow output definitions (#103)

* Template update for nf-core/tools version 2.6

* Template update for nf-core/tools version 2.7.2

* update pipeline name

* update pipeline name

* Template update for nf-core/tools version 2.13.1

* Template update for nf-core/tools version 3.2.0

* Merge branch 'TEMPLATE' into template/3.2.0

* make the pipeline run again

* fix linting

* fix linting

* upload artifacts to v4

* bye bye fastqc

* set the correct min nextflow version in the ci

* update main.nf

* Update conf/modules.config

* update structural.nf

* update bwa index module

* update ngsbits samplegender module

* update subwfs

* update modules.json

* update changelog

* fix subwf test

* fix copy paste error in tests

* move to workflow output definitions

* fix concat outputs

* make output dir dynamic

* fix pipeline tests

* fix subwf tests

* fix pre-commit

* change latest-everything to latest-stable

* bump minimal nextflow version

* use correct version in ci

* fix linting

* fix manta subwf

.github/workflows/ci.yml

@@ -29,7 +29,7 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "24.04.2"
+          - "24.10.0"
           - "latest-everything"
         test:
           - "pipeline_sv"

README.md

@@ -4,7 +4,7 @@
 [![GitHub Actions Linting Status](https://github.com/nf-cmgg/structural/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-cmgg/structural/actions/workflows/linting.yml)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
-[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)
+[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.10.0-23aa62.svg)](https://www.nextflow.io/)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)