v1.11.0 - Generous Ghent

New features

1. Added a new option to the samplesheet (msi). This option takes a boolean to indicate whether or not the MSI status of the sample should be checked. A baseline should be provided using the --msi_baseline parameter to run MSI calling.
2. The Multiqc module now generates branded reports.

Fixes

1. Fixed PED file writing on cloud platforms.
2. Fixed publishing of the MultiQC data directory throwing a NullPointerException.
3. QUAL scores of 256 are no longer converted to . (due to a VCFanno bug).

v1.10.1 - Mighty Mechelen

Fixes

1. Fix a bug where the BED processing failed because of unknown chromosomes.

v1.10.0 - Melodic Mechelen

This release renames the pipeline from nf-cmgg/germline to nf-cmgg/smallvariants to better describe the scope of the pipeline.

Changes

1. Merged the following processes to improve efficiency of the pipeline:
   • VCF index creation modules on output VCFs have been merged into the processes that created these VCFs
   • The filter modules for --filter have been merged
   • BED filtering and intersecting with Regions Of Interest have been merged
2. Added copgt_joint config profile
3. Migrate to the third preview of the workflow output definitions
4. Bumped minimal Nextflow version to 25.04.0
5. Removed --squash-ploidy from the RTG vcfeval process
6. Small stability fixes for runnning on the nomad cluster
7. Added the merged CRAM files to the output of the pipeline. This can be skipped using the --skip_merged_cram_output parameter.
8. Added the filter parameter to the copgt config profiles
9. Added mosdepth QC to the multiQC report

v1.9.3 - Nifty Nieuwkerke

Changes

1. Fix db postprocess in vcf2db module

v1.9.2 - New Nieuwkerke

Changes

1. The pipeline now also outputs the per-base coverage BED file generated by mosdepth per sample
2. Add the --disable_hc_dict_validation parameter that disables sequence dictionary validation in HaplotypeCaller

v1.9.1 - Nice Nieuwkerke

Changes

1. Updated the ROI file in the WES profile from v5 to v6

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.

v1.8.2 - Outstanding Oostkamp

Fixes

1. Fixed some issues where indices were not created
2. Updated the docs

v1.8.1 - Open Oostkamp

Fixes

1. Revert VEP version to v105

v1.8.0 - Optimistic Oostkamp

New features

1. Added watchpath functionality to the pipeline. Add the watch: prefix to a file basename in the samplesheet and the pipeline will automatically wait for the file to be created in the --watchdir directory (the lookup happens recursively)

Changes

1. Bumped the minimal support nextflow version to 24.04.0
2. Bumped all modules to the newest versions
3. The pipeline now also outputs csi indices
4. Rename the master branch to main
5. Low coverage regions (regions with less than 5 reads) are no longer considered for variant calling

Refactors

1. Updated the pipeline to the new linting guidelines
2. Removed check_max in favor of resourceLimits