Releases: uclahs-cds/pipeline-call-sSNV
Releases · uclahs-cds/pipeline-call-sSNV
call-sSNV v4.0.0
Major Changes:
In this release, we change the input files from one template.config to two input files: an input YAML and a template.config. Examples of input YAMLs can be found here. Also, variable sample_name is changed to sample_id.
New Features:
For GATK mutect2 algorithm, we add a germline resource option to filter out the common germline variants. Also, mutect2 can take more than one tumor sample now.
For strelka2 algorithm, we add a --callRegion option to exclude the non-canonical small contigs, thus, largely improve the runtime of WGS samples.
Release 4.0.0-rc.1
Merge pull request #83 from uclahs-cds/maotian-create-release-4.0.0-rc.1 Create Release to 4.0.0-rc.1
call-sSNV v3.0.0
Here are the major changes included in this release:
Changed
- Update .gitignore to exclude molecular files.
- Update F72.config to increase the compute efficiency.
Added
- Add tumor_only_mode in mutect2 options.
call-sSNV v3.0.0-rc.1
Merge pull request #57 from uclahs-cds/maotian-update-GATK-v4.2.4.1 update GATK version to 4.2.4.1 to address log4j2 vulnerabilities
call-sSNV v2.1.1
Added
- Add groups to docker run options.
Fixed
- Add missing lines of checksum process.
call-sSNV v2.1.0 [Deprecated]
Changed
- Updated the GATK version from v4.2.0 to v4.2.2.
- Standardized process names.
- Changed config filenames to F2, F72, and M64.
Added
- Saved logs for the Somaticsniper workflows.
- Add GPL2 license.
- Add pipeline information to the main script.
- Add the checksum file for the final output.
- Add config file for F32 node.
v2.0.0
v1.5.0
Changed
- Mutect2 calls are now scattered by intervals split using GATK SplitIntervals
- Non-canonical regions will be called by default when using Mutect2
- Update branch name in CICD-base.yaml from master to main
Added
- Ability to specify extra arguments for all GATK commands in the Mutect2 workflow
- Steps to index and compress final VCF files