Release 7.0.0

Automatically generated after merging #207.

What's Changed

• Bump external/pipeline-Nextflow-config from 3ec7186 to f3448ac by @dependabot in #145
• Add PlantUML diagram by @Faizal-Eeman in #146
• Add supported Nextflow version to README.md by @Faizal-Eeman in #148
• Standardize description in metadata.yaml by @Faizal-Eeman in #151
• Upgrade to latest static analysis Action by @nwiltsie in #154
• Bump external/pipeline-Nextflow-module from 9db08f0 to 4597ebc by @dependabot in #156
• Bump external/pipeline-Nextflow-config from f3448ac to e703579 by @dependabot in #157
• Bump external/pipeline-Nextflow-module from 4597ebc to ef40c10 by @dependabot in #158
• Bump external/pipeline-Nextflow-config from e703579 to bc3f67e by @dependabot in #159
• Update memory allocations in M64 config by @tyamaguchi-ucla in #161
• Mask version number in config tests by @nwiltsie in #163
• Update dependabot to group common submodules by @nwiltsie in #164
• Bump the pipeline-submodules group across 1 directory with 2 updates by @dependabot in #167
• Add GRIDSS preprocessing by @Faizal-Eeman in #175
• Add GRIDSS Assembly by @Faizal-Eeman in #179
• Add release management workflows by @nwiltsie in #180
• Bump uclahs-cds/tool-PlantUML-action from 1.0.1 to 1 (alias) by @dependabot in #181
• Update cluster reference paths by @nwiltsie in #182
• Add nextflow.config to release management process by @nwiltsie in #183
• Add GRIDSS variant calling by @Faizal-Eeman in #185
• Fix NFTest cases, re-enable config test workflows by @nwiltsie in #189
• CIRCOS Plot by @yashpatel6 in #191
• Update plotting to paramterize genome build by @yashpatel6 in #194
• Bump the pipeline-submodules group across 1 directory with 2 updates by @dependabot in #198
• Add Resource Handling by @Faizal-Eeman in #200
• Add GRIDSS somatic filter by @Faizal-Eeman in #187
• Bump external/pipeline-Nextflow-module from 12f28e4 to 1efa9bf in the pipeline-submodules group by @dependabot in #201
• Add VCF Compression and BCF2VCF Conversion by @Faizal-Eeman in #204
• Enable circos for DELLY by @Faizal-Eeman in #205
• Add GRIDSS2 documentation by @Faizal-Eeman in #203
• Prepare for version 7.0.0 by @boutros-lab-infrastructure-owner in #207

New Contributors

• @tyamaguchi-ucla made their first contribution in #161
• @boutros-lab-infrastructure-owner made their first contribution in #207

Full Changelog: v6.1.0...v7.0.0

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