Release 6.2.0

Automatically generated after merging #238.

What's Changed

• Add pipelines to dependabot by @yashpatel6 in #234
• Merging gitsubmodule package system into one by @yashpatel6 in #235
• Update BAM2FASTQ Version by @yashpatel6 in #237
• Prepare for version 6.2.0 by @boutros-lab-infrastructure-owner in #238

Full Changelog: v6.1.0...v6.2.0

Release 6.1.0

Automatically generated after merging #233.

What's Changed

• Documentation update by @yashpatel6 in #223
• Add sanitization to allow special characters such as underscores in IDs by @yashpatel6 in #225
• Add release management workflows by @nwiltsie in #229
• Update cluster reference paths by @nwiltsie in #230
• Add nextflow.config to release management process by @nwiltsie in #231
• Adding additional test cases by @yashpatel6 in #226
• Prepare for version 6.1.0 by @boutros-lab-infrastructure-owner in #233

New Contributors

• @boutros-lab-infrastructure-owner made their first contribution in #233

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

metapipeline-DNA v6.0.0

What's Changed

• Update dependabot to group common submodules by @nwiltsie in #218
• Pipeline version updates by @yashpatel6 in #220
• Release v6.0.0 by @yashpatel6 in #221

Full Changelog: v6.0.0-rc.6...v6.0.0

metapipeline-DNA v6.0.0-rc.6

What's Changed

• Capture and consolidate detailed logs for each sample by @nwiltsie in #206
• CSV support by @yashpatel6 in #210
• Fix validation bug by @yashpatel6 in #213
• Add optional status_email_address parameter for child pipeline updates by @nwiltsie in #214
• Release 6.0.0-rc.6 by @yashpatel6 in #217

Full Changelog: v6.0.0-rc.5...v6.0.0-rc.6

metapipeline-DNA v6.0.0-rc.5

What's Changed

• Add call-SRC with support for multiple combinations by @yashpatel6 in #204
• Fix WGS submission by @yashpatel6 in #209

Full Changelog: v6.0.0-rc.4...v6.0.0-rc.5

metapipeline-DNA v6.0.0-rc.4

What's Changed

• Bugfixes with task hash and job limiter by @yashpatel6 in #201

Full Changelog: v6.0.0-rc.3...v6.0.0-rc.4

metapipeline-DNA v6.0.0-rc.3

What's Changed

• Status check fixes by @yashpatel6 in #185
• Add call-sCNA to requested_pipelines in template.config by @tyamaguchi-ucla in #190
• Connect expanded intervals from targeted-coverage to downstream pipelines that accept intervals by @yashpatel6 in #184
• Update pipeline versions by @yashpatel6 in #191
• Add support for SRC inputs by @yashpatel6 in #192
• Split validation to allow for streamlined parameter input by @yashpatel6 in #194
• Upgrade to latest static analysis Action by @nwiltsie in #197
• Save sample/patient-specific metapipeline logs by @zhuchcn in #196
• Enable dependabot to keep submodules up-to-date by @nwiltsie in #195
• Release v6.0.0-rc.3 by @yashpatel6 in #200

New Contributors

• @tyamaguchi-ucla made their first contribution in #190

Full Changelog: v6.0.0-rc.2...v6.0.0-rc.3

metapipeline-DNA v6.0.0-rc.2

What's Changed

• Update pipeline versions by @yashpatel6 in #172
• Add generate-SQC-BAM by @yashpatel6 in #174
• Graceful pipeline failure by @yashpatel6 in #175
• Generalize dependencies by @yashpatel6 in #177
• Fix bug with recalibrate-BAM by @yashpatel6 in #179
• Release 6.0.0-rc.2 by @yashpatel6 in #180

Full Changelog: v6.0.0-rc.1...v6.0.0-rc.2

metapipeline-DNA v6.0.0-rc.1

What's Changed

• Convert-BAM2FASTQ 2.0.0-rc.2 by @yashpatel6 in #160
• Align-DNA 10.0.0-rc.1 by @yashpatel6 in #161
• add pipeline-targeted-coverage by @alkaZeltser in #156
• Option to skip recalibrate-BAM by @yashpatel6 in #163
• Sanitize metadata passed to align-DNA by @yashpatel6 in #164
• rename targeted-coverage to calculate-targeted-coverage by @alkaZeltser in #165
• Add pipeline-call-sCNA 3.0.0 by @Faizal-Eeman in #159
• Save input files and logs by @yashpatel6 in #168
• Update testing sample for v6.0.0-rc.1 by @yashpatel6 in #170

New Contributors

• @alkaZeltser made their first contribution in #156

Full Changelog: v5.3.1...v6.0.0-rc.1

metapipeline-DNA v5.3.1

What's Changed

• Pipeline ordering by @yashpatel6 in #152
• Sfitz update call sSNV to 8.0.0-rc.1 by @sorelfitzgibbon in #153
• Release 5.3.1 by @yashpatel6 in #155

New Contributors

• @sorelfitzgibbon made their first contribution in #153

Full Changelog: v5.2.1...v5.3.1