v1.9.0 - Neighborly Nieuwkerke

New features

1. Added the --min_callable_coverage parameter to state what the lowest coverage should for a region to be classified as callable.
2. Added the elprep caller as an alternative to the haplotypecaller.
3. Added full unit tests for all parts that were missing tests.

Changes

1. Added the --squash-ploidy argument to the RTG vcfeval process.
2. Update to nf-core v3.0.1
3. Completely reworked the output directory structure to a more sensible structure. The pipeline can now be run on the same output directory every time and will incrementally add files to the correct family folder. See the output documentation for more info.
4. Migrated to the new workflow output definitions.
5. Bumped the minimal Nextflow version to 24.10.0.
6. Added the somalier reports to the multiQC report.
7. Removed the --output_suffix parameter
8. Added some missing required parameters to the WES and seqplorer profiles

Fixes

1. Validation of all samples now uses an intersect of the golden truth BED files with the BED file used to call the variants. This should fix the WES validation which was broken until this point.
2. A couple of small fixes to the vardict flow.
3. Only use the standard chromosomes for UPDio analysis.
4. Reduced the resources given to some GATK4 modules
5. VCF2DB now uses a seqera container to fix some issues when running it in nomad
6. Dots in sample and family names are now converted to an underscore automatically.