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

v1.7.0 - Tolerant Tongeren

Fixes

1. Automap analysis should now give the correct output files for individuals.

Changes

1. Haplotypecaller will not perform phasing by default now. This can still be turned back on using the --hc_phasing parameter.
2. Removed the WES and WGS profiles.

v1.6.0 - Offbeat Ostend

New features

1. Added UPDio for Uniparental Disomy detection in family samples. This introduces the --updio parameter to turn on this detection and --updio_common_cnvs to supply a common CNVs file to UPDio. The family needs to contain at least one child with its mother and father.
2. Added docs built with MkDocs. See the documentation site here.
3. Added AutoMap to find regions of homozygosity from human samples. This introduces the --automap parameter to turn on this feature and the --automap_repeats, --automap_panel and --automap_panel_name parameters to configure AutoMap (see the parameters docs for more information)

Changes

1. Updated all tests to use snapshots instead.
2. Made the pipeline pluggable to enable the use of it in a meta pipeline.

v1.5.1 - Great Geraardsbergen

v1.5.1 - Great Geraardsbergen - [March 7 2024]

Fixes

1. Fixed an issue with igenomes paths not being casted correctly to their corresponding parameter

v1.5.0 - Amazing Antwerp

Improvements

1. Updated to the nf-core template v2.13.0
2. Updated all GATK modules to 4.5.0.0
3. Moved the pipeline from https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-germline to https://github.com/nf-cmgg/germline

Changes

1. VCF files created with haplotypecaller now have the haplotypecaller tag in the filename instead of gatk4-joint to keep naming consistent

v1.4.2 - Vibrant Veurne

Fixes

1. Set the default ensembl VEP version to 105.0 instead of using dynamic container fetching

v1.4.1 - Lively Leuven

New Features

1. Added the --output_suffix parameter to add a custom suffix to the basename of the output files.
2. Implemented files for the alphamissense plugin of VEP.
3. Added the --only_pass parameter to only output variants that have the PASS flag in the FILTER column. (This is only applied when --filter is also given)
4. Added the --keep_alt_contigs parameter. This will tell the pipeline to not filter out the alternate contigs, which will now be done by default.
5. Add dbsnp Ids to VCFs coming from vardict. This will be done automatically if a dbsnp VCF is given to the pipeline through the --dbsnp parameter.

Improvements

1. Updated the seqplorer profile so that the output filenames are correct for easy import
2. Changed the separator in --vcfanno_resources to ;
   instead of , to allow commas in glob patterns.
3. Removed the reheader step from the vardict subworkflow and added a simple sed substitution to the vardictjava module
4. vcf2db now uses a python 2 environment to increase it's stability

v1.4.0 - Kingly Kortrijk

New Features

1. Added the --callers parameter to specify the variant caller to use. Currently only haplotypecaller and vardict are supported.
2. Added the vardict variant caller.
3. Added the --vardict_min_af parameter to specify the minimum allele frequency for vardict. This option is also available in the samplesheet as vardict_min_af to set it dynamically per sample.
4. Added the --output_genomicsdb option to specify whether a GenomicsDB should be outputted or not. This will be true when using only_merge.
5. Added --normalize options for decomposing and normalizing of variants after calling and genotyping.
6. Added WGS, WES, SeqCap, HyperCap and seqplorer profiles that can be used to set the default parameters for these types of runs.

Improvements

1. Refactored the pipeline to accomodate future additions of variant callers and genotypers
2. Removed a lot of unnecessary bloat
3. Improved GenomicsDBImport (can now be multithreaded and runs a lot faster). This will make very big runs more possible.
4. Changed coverage_fast to mosdepth_slow, reversing the effect of the parameter. By default mosdepth will now be run with --fast-mode. This can be disabled using the new mosdepth_slow parameter.
5. Automatically merge the regions that are within 150 bps of eachother for the variant calling. This way it's ensured that indel calling happens correctly.

Fixes

1. Fixed an issue with the outputting of the validation PNG files, now all three types of PNGs are outputted.
2. Fixed a small issue where VCFs without a sample created by the callers could not be used by bcftools concat, these files will now be filtered from the input of the command.
3. Removed the --maxentscan parameter because this file is automatically present in the container