v6.1.0

What's Changed

• Function updates by @yashpatel6 in #140
• Add standard pipeline workflows by @nwiltsie in #141
• Release 6.1.0 by @yashpatel6 in #143

New Contributors

• @yashpatel6 made their first contribution in #140

Full Changelog: v6.0.0...v6.1.0

v6.0.0

Updates include but not limited to,

• Additional test runs of call-sSV v6.0.0-rc.2 towards release v6.0.0

v6.0.0-rc.2

Major updates,

• DELLY v1.1.3 to v1.2.6
• NFTest added

Other

• Submodules updates

v6.0.0-rc.1

Major updates include:

• Support for CSV input is removed
• YAML input is used
• Sample directory name derived from Tumor ID in BAM header

v5.0.0

Additional test performed on v5.0.0-rc.1 towards v5.0.0.

Major updates in v5.0.0-rc.1 :

• Added Manta SV caller
• Added parameter in template.config to select SV caller
• Migrated from DockerHub to GitHub Packages registry
• Pipeline standardizations

More details on CHANGELOG.md.

v5.0.0-rc.1

Major updates include:

• Added Manta SV caller
• Added parameter in template.config to select SV caller
• Migrated from DockerHub to GitHub Packages registry
• Pipeline standardizations

v4.0.0

Merge release PR #72 into main.

Major updates include but not limited to,

• change input CSV headers: control_sample_bam to normal_bam and tumor_sample_bam to tumor_bam
• add retry mechanism to re-try a process with higher memory
• standardize output filename
• update Delly v1.0.3 to v1.1.3

Refer README.md for more details.

v3.0.0

Merge PR #57 to main.

• Delly upgraded to v1.0.3
• BCFtools upgraded to v1.15.1
• F16 compatibility

v2.0.0

Merge pull request #19 from uclahs-cds/yupan-release-2.0.0

Modified the release date

v1.0.1

Merge pull request #15 from uclahs-cds/yupan-use-docker-delly-0.9.1

Upgade delly version from 0.8.7 to 0.9.1