smallvariants - 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).

- Nextflow
Published by nvnieuwk 6 months ago

smallvariants - v1.10.1 - Mighty Mechelen

Fixes

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

- Nextflow
Published by nvnieuwk 9 months ago

smallvariants - v1.10.0 - Melodic Mechelen

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

- Nextflow
Published by nvnieuwk 9 months ago

smallvariants - v1.9.3 - Nifty Nieuwkerke

Changes

1. Fix db postprocess in vcf2db module

- Nextflow
Published by nvnieuwk about 1 year ago

smallvariants - 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

- Nextflow
Published by nvnieuwk about 1 year ago

smallvariants - v1.9.1 - Nice Nieuwkerke

Changes

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

- Nextflow
Published by nvnieuwk about 1 year ago

smallvariants - 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.

- Nextflow
Published by nvnieuwk about 1 year ago

smallvariants - v1.8.2 - Outstanding Oostkamp

Fixes

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

- Nextflow
Published by nvnieuwk over 1 year ago

smallvariants - v1.8.1 - Open Oostkamp

Fixes

1. Revert VEP version to v105

- Nextflow
Published by nvnieuwk over 1 year ago

smallvariants - 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

- Nextflow
Published by nvnieuwk over 1 year ago

smallvariants - 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.

- Nextflow
Published by nvnieuwk over 1 year ago

smallvariants - 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.

- Nextflow
Published by nvnieuwk almost 2 years ago

smallvariants - 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

- Nextflow
Published by nvnieuwk almost 2 years ago

smallvariants - 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

- Nextflow
Published by nvnieuwk almost 2 years ago

smallvariants - v1.4.2 - Vibrant Veurne

Fixes

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

- Nextflow
Published by nvnieuwk about 2 years ago

smallvariants - 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

- Nextflow
Published by nvnieuwk about 2 years ago

smallvariants - 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

- Nextflow
Published by nvnieuwk about 2 years ago

smallvariants - 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

- Nextflow
Published by nvnieuwk over 2 years ago

smallvariants - v1.2.2 - Benign Brussels

Improvements

Changed the output directory structure to be more bcbio like

- Nextflow
Published by nvnieuwk over 2 years ago

smallvariants - 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

- Nextflow
Published by nvnieuwk over 2 years ago

smallvariants - 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

- Nextflow
Published by nvnieuwk almost 3 years ago

smallvariants - 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

- Nextflow
Published by nvnieuwk almost 3 years ago

smallvariants - 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

- Nextflow
Published by nvnieuwk almost 3 years ago

smallvariants - 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

- Nextflow
Published by nvnieuwk almost 3 years ago

smallvariants - 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

- Nextflow
Published by nvnieuwk over 3 years ago

smallvariants - v1.0.0 - Beautiful Bruges

The first full release of the pipeline!

- Nextflow
Published by nvnieuwk over 3 years ago