Release 8.2.0

Automatically generated after merging #344.

What's Changed

• Bump external/pipeline-Nextflow-module from 4597ebc to ef40c10 by @dependabot in #295
• Bump external/pipeline-Nextflow-config from 795384d to bc3f67e by @dependabot in #294
• Sfitz input vcfs by @sorelfitzgibbon in #274
• add panel of normals by @zhuchcn in #293
• Bump external/pipeline-Nextflow-module from 4597ebc to ef40c10 by @dependabot in #299
• Bump external/pipeline-Nextflow-config from fae7c33 to be1eaf5 by @dependabot in #298
• Update dependabot to group common submodules by @nwiltsie in #302
• update M64 resources by @sorelfitzgibbon in #300
• Add VAF stripplot by @yashpatel6 in #310
• Add release management workflows by @nwiltsie in #317
• Bump uclahs-cds/tool-PlantUML-action from 1.0.0 to 1.0.1 by @dependabot in #318
• Bump the pipeline-submodules group across 1 directory with 2 updates by @dependabot in #309
• add storing of parameters by @sorelfitzgibbon in #312
• fix check for panel of normals and add in log by @sorelfitzgibbon in #319
• Update cluster reference paths by @nwiltsie in #320
• Bump external/pipeline-Nextflow-module from 1cfa9fa to b1d7a78 in the pipeline-submodules group by @dependabot in #321
• use setup_process_afterscript by @sorelfitzgibbon in #314
• Add nextflow.config to release management process by @nwiltsie in #322
• Update versions for five tools by @sorelfitzgibbon in #323
• Sfitz fix single tool runs by @sorelfitzgibbon in #325
• Sfitz add resource handler by @sorelfitzgibbon in #326
• Bump the pipeline-submodules group across 1 directory with 2 updates by @dependabot in #334
• vcf sample id validation by @sorelfitzgibbon in #341
• Bump external/pipeline-Nextflow-module from de9adf9 to 12f28e4 in the pipeline-submodules group by @dependabot in #336
• update nextflow.config by @sorelfitzgibbon in #343
• Prepare for version 8.2.0 by @boutros-lab-infrastructure-owner in #344

New Contributors

• @zhuchcn made their first contribution in #293
• @boutros-lab-infrastructure-owner made their first contribution in #344

Full Changelog: v8.1.0...v8.2.0

v8.1.0

What's Changed

• Bump external/pipeline-Nextflow-config from da8e990 to 3ec7186 by @dependabot in #272
• Add new standard pipeline workflows by @nwiltsie in #275
• Add F32 configtest by @sorelfitzgibbon in #277
• Grant specific permissions to Nextflow tests workflow by @nwiltsie in #280
• Implement refactored Nextflow test workflows by @nwiltsie in #282
• Upgrade to latest static analysis Action by @nwiltsie in #287
• Bump external/pipeline-Nextflow-config from 3ec7186 to af6a606 by @dependabot in #284
• Bump external/pipeline-Nextflow-module from 9db08f0 to 4597ebc by @dependabot in #290
• update resource allocations by @sorelfitzgibbon in #289
• Release 8.1.0 by @sorelfitzgibbon in #291

Full Changelog: v8.0.0...v8.1.0

v8.0.0

What's Changed

• Enable dependabot to keep submodules up-to-date by @nwiltsie in #259
• Sfitz add F8 and adjust F16 and F32 configs by @sorelfitzgibbon in #256
• Bump external/pipeline-Nextflow-module from b0b2798 to 525aa38 by @dependabot in #264
• Bump external/pipeline-Nextflow-config from 27956f3 to 7e10f2c by @dependabot in #263
• update gatk to 4.5.0.0 by @sorelfitzgibbon in #265
• Sfitz pass idx to bam2pileup by @sorelfitzgibbon in #266
• Sfitz update submodules and index file by @sorelfitzgibbon in #269
• Sfitz strelka retry by @sorelfitzgibbon in #270
• Sfitz release 8.0.0 by @sorelfitzgibbon in #271

New Contributors

• @dependabot made their first contribution in #264

Full Changelog: v8.0.0-rc.1...v8.0.0

v8.0.0-rc.1

What's Changed

• Sfitz update resource allocation by @sorelfitzgibbon in #225
• Autofix broken Confluence links by @nwiltsie in #244
• add BigDecimal by @sorelfitzgibbon in #246
• Sfitz remove common checks by @sorelfitzgibbon in #245
• muse update and nftest update by @sorelfitzgibbon in #248
• Sfitz external parse bam by @sorelfitzgibbon in #174
• Sfitz release 8.0.0 rc.1 by @sorelfitzgibbon in #257

New Contributors

• @nwiltsie made their first contribution in #244

Full Changelog: v7.0.0...v8.0.0-rc.1

call-sSNV v7.0.0

What's Changed

• Use bzip2 directly by @yashpatel6 in #241
• Update pipeline release action for publicizing by @yashpatel6 in #242

New Contributors

• @yashpatel6 made their first contribution in #241

Full Changelog: v7.0.0-rc.2...v7.0.0

call-sSNV v7.0.0-rc.2

What's Changed

• Sfitz delay readcount compression by @sorelfitzgibbon in #231
• Sfitz generic resources by @sorelfitzgibbon in #234
• Sfitz fix plot venn bug by @sorelfitzgibbon in #232
• Sfitz nftest assertions by @sorelfitzgibbon in #235
• Sfitz vcf sample orders by @sorelfitzgibbon in #237
• update to MuSE v2.0.3 by @sorelfitzgibbon in #233
• Sfitz release 7.0.0 rc2 and resource allocation update by @sorelfitzgibbon in #239

Full Changelog: v7.0.0-rc.1...v7.0.0-rc.2

v7.0.0-rc.1

What's Changed

• external pipeval by @sorelfitzgibbon in #173
• make SM tags vary between n1 and n2 tumor test BAMs by @sorelfitzgibbon in #177
• split mutect2 VCF to snps, mnps and indels by @sorelfitzgibbon in #170
• fix vcf sample names by @sorelfitzgibbon in #183
• intersect vcfs by @sorelfitzgibbon in #188
• update to muse v2.0.2 and adjust resources by @sorelfitzgibbon in #190
• prep for plot by @sorelfitzgibbon in #196
• Update README.md - fixed spelling typos by @bethneilsen in #214
• no decoy by @sorelfitzgibbon in #211
• plot intersections by @sorelfitzgibbon in #218
• concat vcf by @sorelfitzgibbon in #213
• add maf by @sorelfitzgibbon in #215
• update readme by @sorelfitzgibbon in #223
• compress readcounts by @sorelfitzgibbon in #203
• release candidate 7.0.0 rc1 by @sorelfitzgibbon in #229

New Contributors

• @bethneilsen made their first contribution in #214

Full Changelog: v6.0.0...v7.0.0-rc.1

call-sSNV v6.0.0

What's Changed

• Change intermediate directory and task.index by @maotian06 in #128
• Switch Docker Hub images to GitHub packages by @maotian06 in #127
• update to use SAMtools 1.16.1 by @sorelfitzgibbon in #135
• Add contamination file option by @maotian06 in #129
• Sfitzgibbon standardize readme by @sorelfitzgibbon in #136
• Sfitzgibbon add filtering stats output by @sorelfitzgibbon in #139
• update submodules and use set_resources_allocation from common by @sorelfitzgibbon in #140
• restore mistakenly removed F2.config by @sorelfitzgibbon in #142
• Sfitz add pipeline steps by @sorelfitzgibbon in #147
• correcting the changelog with fixed release by @sorelfitzgibbon in #151
• setup nftest a-mini by @sorelfitzgibbon in #153
• Increase muse retry memory by @sorelfitzgibbon in #156
• updated to use muse2.0.1 with sump parallelization by @sorelfitzgibbon in #157
• Sfitz roll back MuSE by @sorelfitzgibbon in #164
• Sfitz add muse flowchart by @sorelfitzgibbon in #161
• update to GATK v4.4.0.0 by @sorelfitzgibbon in #167
• Sfitz add mutect flowchart by @sorelfitzgibbon in #168
• Increase memory for GATK LearnReadOrientation by @sorelfitzgibbon in #165

New Contributors

• @sorelfitzgibbon made their first contribution in #135

Full Changelog: v5.0.0...v6.0.0

call-sSNV v6.0.0-rc.1

Changed

• Update README: add Pipeline Steps and Tool descriptions
• Update to use set_resources_allocation from pipeline-Nextflow-config repo
• Update SAMtools to v1.16.1
• Switch Docker Hub images to GitHub packages.
• Remove redundant directories in log output directories and intermediate directories.
• Specify task.index in log output directories.

Added

• Add QC output filteringStats.tsv from Mutect2's process run_FilterMutectCalls_GATK.
• Add contamination_table input to input.yaml. Contamination estimate table was generated from CalculateContamination from GATK.

call-sSNV v5.0.0

What's Changed

• Add retry.config by @maotian06 in #86
• Add filename module to standardize output filename by @maotian06 in #112
• Add Index Module by @maotian06 in #107
• Change Input YAML Structure by @maotian06 in #116
• Add MuSE workflow by @maotian06 in #113
• Add pipeline-release.yaml and version bump 5.0.0 by @maotian06 in #125

Full Changelog: v4.0.1...v5.0.0