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‎CHANGELOG.md‎

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# Changelog
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All notable changes to this project will be documented in this file.
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The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
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and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
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## [Unreleased]
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## [8.2.0] - 2025-05-01
9+
10+
### Added
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12+
- Use `methods.setup_process_afterscript()` for process logs
13+
- Output pipeline parameters to log directory using `store_object_as_json`
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- Add `panel_of_normals_vcf` for MuTect2.
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- Add `a_mini-all-tools-vcf-input` to `nftest`
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- Add option to input VCFs for intersection
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- Add VAF stripplot for variant overlaps across tools
18+
819
### Changed
20+
21+
- Remove cluster paths from README
22+
- Avoid VAF divide by zero error
23+
- Switch to generalized resource handling
924
- Update NFTest paths
1025
- Fix single tool run logic
1126
- Update PipeVal 4.0.0-rc.2 -> 5.1.0
@@ -16,36 +31,33 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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- Update NFtest for new tool versions
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- Set VAF plot y-limit based on max adjusted VAF
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19-
### Added
20-
- Use `methods.setup_process_afterscript()` for process logs
21-
- Output pipeline parameters to log directory using `store_object_as_json`
22-
- Add `panel_of_normals_vcf` for MuTect2.
23-
- Add `a_mini-all-tools-vcf-input` to `nftest`
24-
- Add option to input VCFs for intersection
25-
- Add VAF stripplot for variant overlaps across tools
26-
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### Fixed
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- Avoid warning when run without panel of normals
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36+
- Avoid warning when run without panel of normals
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## [8.1.0] - 2024-05-15
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### Added
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3342
- Add workflow to build and publish documentation to GitHub Pages
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- Add workflow to run Nextflow configuration regression tests
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- Add one regression test
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- Add workflow to respond to "/fix-tests" comments
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### Fixed
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- Grant explicit permissions for Nextflow configuration test workflow
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- Update Nextflow configuration test workflows
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4247
### Changed
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4349
- Update M64 resource allocations
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- Update resource allocations
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### Fixed
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54+
- Grant explicit permissions for Nextflow configuration test workflow
55+
- Update Nextflow configuration test workflows
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4657
## [8.0.0] - 2024-01-29
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4859
### Changed
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4961
- `Strelka2` retry triggered by error code `1`
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- Pass reference index to `SomaticSniper` processes
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- Use external `indexFile` function
@@ -56,6 +68,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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## [8.0.0-rc.1] - 2023-12-13
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### Changed
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5972
- Sample names sanitized for all output
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- Sample names parsed from input BAMs
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- Update `MuSE` to `v2.0.4`
@@ -65,15 +78,18 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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## [7.0.0] - 2023-10-18
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### Changed
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6882
- Use `bzip2` directly for compression
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## [7.0.0-rc.2] - 2023-10-05
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7286
### Added
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7388
- Add .github/CODEOWNERS
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- Add check for MuSE or Mutect2 on F2 node
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7691
### Changed
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7793
- Resource allocations changed for F32 and F72
7894
- Update `MuSE` to `v2.0.3`
7995
- Reorder all VCFs before intersection
@@ -83,10 +99,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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## [7.0.0-rc.1] - 2023-08-28
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### Changed
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- Update plot-venn.R to work with all numbers of algorithms greater than two
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89102
### Added
103+
90104
- Custom resource allocation updates through configuration parameters
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- Add assertions to `nftest`
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- Add compression of `SomaticSniper` `bam-readcount` output and move to `intermediate` directory
@@ -101,6 +115,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
101115
- Add `split_VCF_bcftools` to `Mutect2` workflow, separating SNVs, MNVs and Indels
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103117
### Changed
118+
119+
- Update plot-venn.R to work with all numbers of algorithms greater than two
104120
- Fix CPU allocation behavior with Docker
105121
- Remove redundant directories in Intersect log output directories
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- Change compression of intersect MAF file to bzip2
@@ -120,164 +136,241 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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## [6.0.0] - 2023-04-05
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### Added
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123140
- Add Mutect2 flow chart
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- Add plantUML action and MuSE flow chart
125142
- Add NF-test
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127144
### Changed
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128146
- Update LearnReadOrientationModel allocated memory and cpus
129147
- Update to GATK v4.4.0.0
130148
- Update `MuSE` retry add memory to 48GB
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- Changed `output_dir` to `output_dir_base` (`methods.config` and `main.nf`)
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133151
### Fixed
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134153
- Specify empty string as default for bgzip and tabix extra args
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## [6.0.0-rc.1] - 2023-02-08
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157+
### Added
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- Add QC output `filteringStats.tsv` from Mutect2's process `run_FilterMutectCalls_GATK`.
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- Add `contamination_table` input to `input.yaml`. Contamination estimate table was generated from [CalculateContamination](https://gatk.broadinstitute.org/hc/en-us/articles/9570322332315-CalculateContamination) from GATK.
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137162
### Changed
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138164
- Update `README`: add Pipeline Steps and Tool descriptions
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- Update to use `set_resources_allocation` from pipeline-Nextflow-config repo
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- Update SAMtools to v1.16.1
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- Switch Docker Hub images to GitHub packages.
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- Remove redundant directories in log output directories and intermediate directories.
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- Specify `task.index` in log output directories.
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### Added
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- Add QC output `filteringStats.tsv` from Mutect2's process `run_FilterMutectCalls_GATK`.
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- Add `contamination_table` input to `input.yaml`. Contamination estimate table was generated from [CalculateContamination](https://gatk.broadinstitute.org/hc/en-us/articles/9570322332315-CalculateContamination) from GATK.
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## [5.0.0] - 2022-10-04
150-
### Changed
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- Change index_VCF_tabix process using git submodule from [pipeline-Nextflow-module](https://github.com/uclahs-cds/pipeline-Nextflow-module).
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- Standardize output filenames using `generate_standardized_filename` module from [pipeline-Nextflow-module](https://github.com/uclahs-cds/pipeline-Nextflow-module/tree/main/modules/common/generate_standardized_filename).
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- Change the `input.yaml` structure to allow separate sample_ids for normal and tumor BAMs.
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### Added
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- Add retry.config using git submodule from [pipeline-Nextflow-config](https://github.com/uclahs-cds/pipeline-Nextflow-config) to enable processes to retry with more memory.
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- Add [MuSE](https://github.com/wwylab/MuSE) workflow.
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- Add `pipeline-release.yaml` to [workflow](.github/workflows).
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### Changed
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181+
- Change index_VCF_tabix process using git submodule from [pipeline-Nextflow-module](https://github.com/uclahs-cds/pipeline-Nextflow-module).
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- Standardize output filenames using `generate_standardized_filename` module from [pipeline-Nextflow-module](https://github.com/uclahs-cds/pipeline-Nextflow-module/tree/main/modules/common/generate_standardized_filename).
183+
- Change the `input.yaml` structure to allow separate sample_ids for normal and tumor BAMs.
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## [4.0.1] - 2022-06-24
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161187
### Changed
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162189
- Update PR template.
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### Fixed
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- Fix the bug with M64 detection.
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- Fix the bug with interval list input.
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## [4.0.0] - 2022-06-13
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169198
### Changed
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- Update `README.md` to apply the recent changes.
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- Update the YAML input structure.
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### Fixed
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174205
- Add the decoy file for `params.germline_resource_gnomad_vcf`.
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## [4.0.0-rc.1] - 2022-05-13
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### Changed
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- Change the input files to YAML and template.config.
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- Change the `sample_name` to `sample_id`.
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- Standardize the repository structure.
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### Added
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183211
- Add Mutect2's multiple samples option into the pipeline.
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- Add germline resource to Mutect2.
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- Add `--callRegion` option to Stelka2 algorithm.
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- Add Manta and Strelka2's intermediate files.
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- Add schema.config using git submodule from [pipeline-Nextflow-config](https://github.com/uclahs-cds/pipeline-Nextflow-config) to check if params are valid.
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## [3.0.0] - 2022-03-01
190217
### Changed
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- Update .gitignore to exclude molecular files.
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- Update F72.config to increase the compute efficiency.
218+
219+
- Change the input files to YAML and template.config.
220+
- Change the `sample_name` to `sample_id`.
221+
- Standardize the repository structure.
222+
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## [3.0.0] - 2022-03-01
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### Added
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194227
- Add tumor_only_mode in mutect2 options.
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- Add Mutect2's orientation bias filter.
196-
### Fixed
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230+
### Changed
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232+
- Update .gitignore to exclude molecular files.
233+
- Update F72.config to increase the compute efficiency.
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## [3.0.0-rc.1] - 2022-01-07
236+
199237
### Changed
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200239
- Standardize the output directory.
201240
- Standardize timestamp according to ISO8601.
202241
- Update PipeVal to 2.1.6.
203242
- Rename Docker images and remove Dockerfiles.
204243
- Apply the config file standardization.
244+
205245
### Security
206-
- Update GATK to 4.2.4.1 to address Log4j critical vulnerability [GHSA-jfh8-c2jp-5v3q](https://github.com/advisories/GHSA-jfh8-c2jp-5v3q) and other newly discovered log4j2 vulnerabilities.
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247+
- Update GATK to 4.2.4.1 to address Log4j critical vulnerability [GHSA-jfh8-c2jp-5v3q](https://github.com/advisories/GHSA-jfh8-c2jp-5v3q) and other newly discovered log4j2 vulnerabilities.
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209249
## [2.1.1] - 2021-10-15
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### Changed
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### Added
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- Add groups to docker run options.
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### Fixed
215-
- Add missing lines of checksum process.
253+
- Add groups to docker run options.
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### Deprecated
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218257
- Deprecate version 2.1.0.
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### Fixed
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261+
- Add missing lines of checksum process.
262+
220263
## [2.1.0] - 2021-10-13
221-
### Changed
222-
- Update the GATK version from 4.2.0 to 4.2.2.
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- Standardize process names.
224-
- Change config filenames to F2, F72, and M64.
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### Added
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227267
- Save logs for the Somaticsniper workflows.
228268
- Add GPL2 license.
229269
- Add pipeline information to the main script.
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- Add the checksum file for the final output.
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- Add the config file for F32 node.
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## [v2.0.0] - 2021-08-19
234273
### Changed
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- Allow multiple algorithms to run in one pipeline run.
274+
275+
- Update the GATK version from 4.2.0 to 4.2.2.
276+
- Standardize process names.
277+
- Change config filenames to F2, F72, and M64.
278+
279+
## [2.0.0] - 2021-08-19
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### Added
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238283
- Add pattern to strelka2's filter_vcf_pass publishDir.
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285+
### Changed
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287+
- Allow multiple algorithms to run in one pipeline run.
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240289
### Fixed
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241291
- Fix nextflow.config throwing Exception: string interpolation required double quotes.
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## [v1.5.0] - 2021-06-18
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## [1.5.0] - 2021-06-18
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295+
### Added
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297+
- Specify extra arguments for all GATK commands in the Mutect2 workflow.
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- Add steps to index and compress final VCF files.
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244300
### Changed
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245302
- Mutect2 calls are now scattered by intervals split using GATK SplitIntervals.
246303
- Non-canonical regions will be called by default when using Mutect2.
247304
- Update branch name in CICD-base.yaml from master to main.
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### Added
250-
- Specify extra arguments for all GATK commands in the Mutect2 workflow.
251-
- Add steps to index and compress final VCF files.
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## [1.4.0] - 2021-04-27
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## [v1.4.0] - 2021-04-27
254308
### Added
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255310
- Save logs for the Strelka2 and Mutect2 workflows.
256311
- Create and backfill CHANGELOG.
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258313
### Changed
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259315
- Mutect2 calls are now scattered by chromosomes.
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261-
## [v1.3.0] - 2021-04-05
317+
## [1.3.0] - 2021-04-05
318+
262319
### Added
320+
263321
- Add the Mutect2 algorithm.
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265-
## [v1.2.0] - 2021-03-11
323+
## [1.2.0] - 2021-03-11
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266325
### Added
326+
267327
- Add the strelka2 algorithm.
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### Changed
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270331
- Index files are assumed to exist in the same directory as bam/reference files.
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## [1.1.0] - 2021-02-16
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273335
### Changed
336+
274337
- Pipeline rewritten in DSL2.
275338
- Docker run as user.
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277340
## [1.0.0] - 2020-11-24
341+
278342
### Fixed
343+
279344
- Fix bug to correctly filter pileup file in varFilter step.
280345

281346
## [0.0.1-beta] - 2020-11-12
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282348
### Added
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283350
- The is the first beta release of the call-sSNV pipeline. It implements only 1 SNV caller, somatic sniper. Input and output validation and dynamic resource allocation is implemented.
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[0.0.1-beta]: https://github.com/uclahs-cds/pipeline-call-sSNV/releases/tag/v0.0.1-beta
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[1.0.0]: https://github.com/uclahs-cds/pipeline-call-sSNV/compare/v0.0.1-beta...v1.0.0
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[1.1.0]: https://github.com/uclahs-cds/pipeline-call-sSNV/compare/v1.0.0...v1.1.0
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[1.2.0]: https://github.com/uclahs-cds/pipeline-call-sSNV/compare/v1.1.0...v1.2.0
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[1.3.0]: https://github.com/uclahs-cds/pipeline-call-sSNV/compare/v1.2.0...v1.3.0
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[1.4.0]: https://github.com/uclahs-cds/pipeline-call-sSNV/compare/v1.3.0...v1.4.0
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[1.5.0]: https://github.com/uclahs-cds/pipeline-call-sSNV/compare/v1.4.0...v1.5.0
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[2.0.0]: https://github.com/uclahs-cds/pipeline-call-sSNV/compare/v1.5.0...v2.0.0
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[2.1.0]: https://github.com/uclahs-cds/pipeline-call-sSNV/compare/v2.0.0...v2.1.0
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[2.1.1]: https://github.com/uclahs-cds/pipeline-call-sSNV/compare/v2.1.0...v2.1.1
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[3.0.0]: https://github.com/uclahs-cds/pipeline-call-sSNV/compare/v3.0.0-rc.1...v3.0.0
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[3.0.0-rc.1]: https://github.com/uclahs-cds/pipeline-call-sSNV/compare/v2.1.1...v3.0.0-rc.1
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[4.0.0]: https://github.com/uclahs-cds/pipeline-call-sSNV/compare/v4.0.0-rc.1...v4.0.0
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[4.0.0-rc.1]: https://github.com/uclahs-cds/pipeline-call-sSNV/compare/v3.0.0...v4.0.0-rc.1
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[4.0.1]: https://github.com/uclahs-cds/pipeline-call-sSNV/compare/v4.0.0...v4.0.1
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[5.0.0]: https://github.com/uclahs-cds/pipeline-call-sSNV/compare/v4.0.1...v5.0.0
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[6.0.0]: https://github.com/uclahs-cds/pipeline-call-sSNV/compare/v6.0.0-rc.1...v6.0.0
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[6.0.0-rc.1]: https://github.com/uclahs-cds/pipeline-call-sSNV/compare/v5.0.0...v6.0.0-rc.1
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[7.0.0]: https://github.com/uclahs-cds/pipeline-call-sSNV/compare/v7.0.0-rc.2...v7.0.0
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[7.0.0-rc.1]: https://github.com/uclahs-cds/pipeline-call-sSNV/compare/v6.0.0...v7.0.0-rc.1
372+
[7.0.0-rc.2]: https://github.com/uclahs-cds/pipeline-call-sSNV/compare/v7.0.0-rc.1...v7.0.0-rc.2
373+
[8.0.0]: https://github.com/uclahs-cds/pipeline-call-sSNV/compare/v8.0.0-rc.1...v8.0.0
374+
[8.0.0-rc.1]: https://github.com/uclahs-cds/pipeline-call-sSNV/compare/v7.0.0...v8.0.0-rc.1
375+
[8.1.0]: https://github.com/uclahs-cds/pipeline-call-sSNV/compare/v8.0.0...v8.1.0
376+
[8.2.0]: https://github.com/uclahs-cds/pipeline-call-sSNV/compare/v8.1.0...v8.2.0

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