v1.3.0 - Happy Hasselt

New Features

1. Added the --only_call parameter. Specifying this parameter tells the pipeline to only do variant calling and skip all post-processing. This will only output the GVCFs and files created to help variant calling.
2. The samplesheet is now also in the output folder.
3. Added an option --only_merge to tell the pipeline to create genomicsdbs and stop running there
4. Get regions from the GVCF instead of CRAM for joint genotyping. This removes the need to supply a CRAM file when a GVCF file has been used as input.

Improvements

1. Updated nf-validation to v0.2.1.
2. Updated the samtools/merge tool to the nf-core version. This increases the efficiency and disk space usage of the tool.

Fixes

1. Fixed an error where the truth VCFs caused a join error when the same sample was given multiple times
2. Updated some outdated error messages

v1.2.2 - Benign Brussels

Improvements

Changed the output directory structure to be more bcbio like

v1.2.1 - Balanced Brussels

New Features

1. Added support for the nf-validation plugin.
2. Haplotypecaller dragen mode will be automatically disabled when not using a dragstr model.

Bug fixes

1. Removed bedtools/jaccard
2. Fixed some patterns in the parameter JSON schema (since they are actually used now)
3. Fixed a breaking bug where mosdepth didn't output the callable regions (this makes v1.2.0 deprecated, please use v1.2.1 instead)

Improvements

1. Genomicsdbs aren't scattered now, this increases the precision of the analyis by almost 3% at the cost of a bit longer runtimes
2. Actually do the validation on the output VCFs now instead the freshly called GVCFs
3. Improved the efficiency of the VEP run by scattering more efficiently on the amount of variants instead of the chromosomes

v1.2.0 - Brave Brussels

WARNING: This version contains a fatal bug with Mosdepth which causes the pipeline to only call on low coverage regions. Please use the dev branch in the meantime.

New Features

1. Added a --coverage_fast <true/false> flag which can be used to run mosdepth in fast mode. This flag will also make sure that only the quantized bed from mosdepth is present in the output directory for each WGS individual, otherwise it will output everything
2. Added the possibility to give GVCF files as inputs and immediately go to the joint-genotyping. This is especially useful for the cases where several samples should be combined. This way the variant calling doesn't need to be re-run. Beware though that a CRAM file should still be given to generate the BED files used for the scatter/gathering. The new header names are gvcf and tbi where gvcf is used to give the GVCF and tbi is used to give its index.
3. Added bedtools jaccard to the validation.
4. Added a Dockerfile which creates an image that is able to run a full pipeline run inside of it.
5. Added better documentation

Improvements

1. Updated the scattering again: it now follows this workflow:
   • Sort and merge overlapping intervals of given ROI BED files (WES only)
   • Create a BED file with callable regions using mosdepth
   • Intersect the callable regions BED with the ROI BED (WES only)
   • Split the resulting BED file (or the callable regions BED for WGS) into evenly sized BED files (amount is specified with --scatter_count)
   • Run HaplotypeCaller in parallel using these regions
   • Merge and sort the BED files of all individuals in a family
   • Split the merged BED file into evenly sized BED files (amount is specified with --scatter_count times the family size)
   • Run GenomicsDBImport and GenotypeGVCFs in parallel using these regions
2. Updated the resource requirements of GenomicsDBImport and GenotypeGVCFs to be more efficient (and more cluster friendly)
3. Removed ReblockGVCFs (this wasn't worth it and we save the raw GVCFs)
4. Added --merge_distance <integer> to decrease the amount of intervals passed to genomicsdbimport. Increase this value if GenomicsDBImport is running slow.
5. Renamed --use_dragstr_model to --dragstr.

Bug fixes

1. Fixed a warning showing up when running with --dragstr false
2. Add --infer flag to somalier relate when no PED file is given

v1.1.2 - Groovy Ghent

New features

1. Added a parameter for setting the splitting depth threshold --split_threshold FLOAT

Changes

1. Change the default splitting threshold to 0.2 instead of 0.3

v1.1.1 - Golden Ghent

Changes

1. Set the default of --validate to false

Bug fixes

1. Fixed a bug with ensembl VEP. Filenames of the alt contigs should now have a _alt suffix instead of all alt contigs.
2. Added file-exist check to the sdf file
3. Fixed the scattering when using alt contigs

v1.1.0 - Glorious Ghent

! WES support has been temporarily disabled, but is planned to be re-added in the next major release !

New Features

1. Added support for samples that aren't part of a family. Just leave the ped and family_id input fields in the samplesheet empty for a sample to be treated like this. This sample will go through exactly the same workflow but will be emitted as a single-sample VCF.
2. Added dump functionality to lots of channels.
3. Added the dbsnp option to GATK HaplotypeCaller. use --dbsnp and --dbsnp_tbi to supply these VCFs.
4. Added the vcf_extract_somalier subworkflow to the pipeline. This also creates PED files inferred from the input multi-sample VCF.
5. Added a validation subworkflow. All files that have a VCF in the truth_vcf column of the input samplesheet will be validated against this VCF. This can be turned off by supplying the --validate false flag to the pipeline run.

Improvements

1. Improved the scatter/gather logic. This is now done with goleft indexsplit to define chunks of even coverage. The genotyping scattering now happens with bedtools makewindows. This creates chunks of even regions from the merged BED files for the family. By passing a padding of about 20 bps to the genotype tools, we make sure all variants on the edges of these regions are also genotyped. Duplicates are removed later when running bcftools concat
2. Refactored a lot of the code to maintain the same style over the whole pipeline.
3. Updated the minimum Nextlow version to 22.10.5 to make sure S3 staging works perfectly.
4. The post_processing subworklow has been renamed to the better suiting joint_genotyping subworkflow. reblockgvcf has been moved to germline_variant_calling and the filter and reheadering has been moved to the main workflow.
5. Merging VCFs of the same family now happens with GATK GenomicsDBImport instead of GATK MergeGVCFs or bcftools merge. This gives more reliable results.
6. Improved the handling of vcfanno
7. The PED headers can now be added to all the output VCFs that are part of a family instead of only those that were given a PED file as input. The PED file used is created using somalier relate. This feature can be turned on using the --add_ped true argument. This doesn't happen by default.

Bug fixes

1. Fixed some issues when both the ped and family_id were given for a sample.
2. Fixed the PED input for rtgtools_pedfilter (-9 isn't recognized as unknown by the tool. Now these will be automatically converted to 0 before this tool)
3. Fixed issues with the DBsnp index not being created correctly
4. Fixed wrongly formed joins and added checks for mismatches and duplicates

v1.0.1 - Happy Hollebeke

Changes

• Upgraded to nf-core v2.6 template

Fixes

• Fixed the ensemblvep version (was 104.1 before and is now 105.0)
• Updated the label of gatk4/calibratedragstrmodel to process_high to match the requirements for bigger inputs

v1.0.0 - Beautiful Bruges

The first full release of the pipeline!