Releases: uclahs-cds/pipeline-recalibrate-BAM
Releases · uclahs-cds/pipeline-recalibrate-BAM
recalibrate-BAM v1.0.1
What's Changed
- Fixup accidental push by @nwiltsie in #59
- Add requirements to README by @nwiltsie in #63
- Final prep for publication by @nwiltsie in #64
- Implement refactored Nextflow test workflows by @nwiltsie in #62
- Upgrade to latest static analysis Action by @nwiltsie in #67
- Bump external/pipeline-Nextflow-config from
f3448ac
to795384d
by @dependabot in #68 - Bump external/pipeline-Nextflow-module from
9db08f0
to4597ebc
by @dependabot in #69 - Resolve intervals when needed by @yashpatel6 in #73
Full Changelog: v1.0.0...v1.0.1
recalibrate-BAM v1.0.0
What's Changed
- Autofix broken Confluence links by @nwiltsie in #35
- Make output deterministic, add NFTest case by @nwiltsie in #36
- Update PR template by @nwiltsie in #37
- Enable dependabot to update submodules by @nwiltsie in #40
- Bump external/pipeline-Nextflow-module from
4bc4336
tob0b2798
by @dependabot in #41 - Bump external/pipeline-Nextflow-config from
c77aeca
toedfc2c2
by @dependabot in #42 - Update flow diagram, add details to README by @nwiltsie in #39
- Allow input of recalibration tables by @yashpatel6 in #45
- Remove local set_env and check_limits methods by @nwiltsie in #46
- Bump external/pipeline-Nextflow-config from
edfc2c2
to1960eaa
by @dependabot in #44 - Use store_object_as_json method to store parameters by @nwiltsie in #47
- Add documentation action by @nwiltsie in #53
- Add Nextflow configuration regression tests by @nwiltsie in #55
- Bump external/pipeline-Nextflow-module from
b0b2798
to9db08f0
by @dependabot in #49 - Bump external/pipeline-Nextflow-config from
1960eaa
tof3448ac
by @dependabot in #56 - Release
v1.0.0
by @yashpatel6 in #58
New Contributors
- @dependabot made their first contribution in #41
Full Changelog: v1.0.0-rc.4...v1.0.0
recalibrate-BAM v1.0.0-rc.4
[Fixed]
- Resource updater to allow update for all processes
- Channel handling to save contamintion estimate files
recalibrate-BAM v1.0.0-rc.3
recalibrate-BAM v1.0.0-rc.2
recalibrate-BAM v1.0.0-rc.1
[Added]
- Basic configuration setup
- Input YAML templates and handling
- Per-patient input YAML handling
- Interval splitting process, either per-chromosome by default or scattered
- Indel Realignment workflow
- BQSR workflow
- Merging workflow
- Contamination and depth of coverage processes
- Input deletion
- Intermediate file deletion
- Schema validation
- Documentation