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nf-cmgg/germline: Changelog

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

v1.7.0 - Tolerant Tongeren - [August 9 2024]

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 - [April 29 2024]

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 - [March 7 2024]

Fixes

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

v1.5.0 - Amazing Antwerp - [March 4 2024]

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 no have the haplotypecaller tag in the filename instead of gatk4-joint to keep naming consistent

v1.4.2 - Vibrant Veurne - [January 25 2024]

Fixes

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

v1.4.1 - Lively Leuven - [January 15 2024]

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 - [December 6 2023]

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

v1.3.0 - Happy Hasselt - [July 10 2023]

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 - [June 12 2023]

Improvements

Changed the output directory structure to be more bcbio like

v1.2.1 - Balanced Brussels - [June 5 2023]

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 - [May 5 2023]

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 - [Mar 21 2023]

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 - [Mar 20 2023]

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 - [Mar 14 2023]

New Features

  1. BED file input is new optional (The regions are created from the FASTA index). Providing a BED file is still preffered for the most optimal runs.
  2. 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.
  3. Added dump functionality to lots of channels.
  4. Added the dbsnp option to GATK HaplotypeCaller. use --dbsnp and --dbsnp_tbi to supply these VCFs.
  5. Added the vcf_extract_somalier subworkflow to the pipeline. This also creates PED files inferred from the input multi-sample VCF.
  6. 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 - [Oct 7 2022]

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 - [Oct 3 2022]

Added

  • Full release of the pipeline

v1.0dev - [May 31 2022]

Initial release of nf-cmgg/germline, created with the nf-core template.