Release 1.0.2

Automatically generated after merging #86.

What's Changed

• Bump external/pipeline-Nextflow-module from 4597ebc to ef40c10 by @dependabot in #72
• Bump external/pipeline-Nextflow-config from 795384d to bc3f67e by @dependabot in #71
• Use methods.setup_process_afterscript() for process logs by @nwiltsie in #76
• Group pipeline-Nextflow-* modules together for dependabot by @nwiltsie in #74
• Bump external/pipeline-Nextflow-config from bc3f67e to be1eaf5 by @dependabot in #75
• Use wildcards in dependabot submodule grouping by @nwiltsie in #79
• Bump the pipeline-submodules group across 1 directory with 2 updates by @dependabot in #81
• Organizational and cleanup tweaks by @nwiltsie in #82
• Bump external/pipeline-Nextflow-module from 537da32 to 1cfa9fa in the pipeline-submodules group by @dependabot in #83
• Add release management workflows by @nwiltsie in #85
• Prepare for version 1.0.2 by @boutros-lab-infrastructure-owner in #86

New Contributors

• @boutros-lab-infrastructure-owner made their first contribution in #86

Full Changelog: v1.0.1...v1.0.2

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 to 795384d by @dependabot in #68
• Bump external/pipeline-Nextflow-module from 9db08f0 to 4597ebc 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 to b0b2798 by @dependabot in #41
• Bump external/pipeline-Nextflow-config from c77aeca to edfc2c2 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 to 1960eaa 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 to 9db08f0 by @dependabot in #49
• Bump external/pipeline-Nextflow-config from 1960eaa to f3448ac 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

CHANGELOG

[Fixed]

• Resource updater to allow update for all processes
• Channel handling to save contamintion estimate files

recalibrate-BAM v1.0.0-rc.3

CHANGELOG

[Added]

• Customization options for which input BAMs to delete with metapipeline

recalibrate-BAM v1.0.0-rc.2

CHANGELOG

[Added]

• Custom resource allocation updates through configuration parameters

recalibrate-BAM v1.0.0-rc.1

CHANGELOG

[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