Releases · nf-cmgg/germline

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

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.
Added dump functionality to lots of channels.
Added the dbsnp option to GATK HaplotypeCaller. use --dbsnp and --dbsnp_tbi to supply these VCFs.
Added the vcf_extract_somalier subworkflow to the pipeline. This also creates PED files inferred from the input multi-sample VCF.
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.

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
Refactored a lot of the code to maintain the same style over the whole pipeline.
Updated the minimum Nextlow version to 22.10.5 to make sure S3 staging works perfectly.
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.
Merging VCFs of the same family now happens with GATK GenomicsDBImport instead of GATK MergeGVCFs or bcftools merge. This gives more reliable results.
Improved the handling of vcfanno
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.

Fixed some issues when both the ped and family_id were given for a sample.
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)
Fixed issues with the DBsnp index not being created correctly
Fixed wrongly formed joins and added checks for mismatches and duplicates

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