diff --git a/CHANGELOG.md b/CHANGELOG.md index d033b836..0984fed1 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,15 +5,22 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). ## [Unreleased] + ### Added - Add Mutect2 flow chart - Add plantUML action and MuSE flow chart - Add NF-test + ### Changed +- Update LearnRaadOrientationModel allocated memory +- Update to use `MuSE` v2.0.1 with `MuSE sump` parallelization - Update to GATK v4.4.0.0 - Update `MuSE` retry add memory to 48GB - Changed `output_dir` to `output_dir_base` (`methods.config` and `main.nf`) +### Fixed +- Specify empty string as default for bgzip and tabix extra args + ## [6.0.0-rc.1] - 2023-02-08 ### Changed - Update `README`: add Pipeline Steps and Tool descriptions diff --git a/config/F16.config b/config/F16.config index 5798edd5..6abe75b2 100644 --- a/config/F16.config +++ b/config/F16.config @@ -60,8 +60,8 @@ process { } } withName: run_LearnReadOrientationModel_GATK { - cpus = 4 - memory = 8.GB + cpus = 1 + memory = 16.GB retry_strategy { memory { strategy = 'exponential' diff --git a/config/F32.config b/config/F32.config index 64c6b62d..d8f2a7a8 100644 --- a/config/F32.config +++ b/config/F32.config @@ -60,8 +60,8 @@ process { } } withName: run_LearnReadOrientationModel_GATK { - cpus = 4 - memory = 8.GB + cpus = 1 + memory = 16.GB retry_strategy { memory { strategy = 'exponential' diff --git a/config/F72.config b/config/F72.config index 15301c73..6b0321ae 100644 --- a/config/F72.config +++ b/config/F72.config @@ -59,8 +59,8 @@ process { } } withName: run_LearnReadOrientationModel_GATK { - cpus = 4 - memory = 8.GB + cpus = 1 + memory = 16.GB retry_strategy { memory { strategy = 'exponential' diff --git a/config/schema.yaml b/config/schema.yaml index a462f37e..ca2ded4c 100644 --- a/config/schema.yaml +++ b/config/schema.yaml @@ -66,6 +66,18 @@ filter_mutect_calls_extra_args: required: false allow_empty: true help: 'Additional arguments for the FilterMutectCalls command' +bgzip_extra_args: + type: 'String' + required: false + allow_empty: true + default: '' + help: 'Additional arguments for bgzip command' +tabix_extra_args: + type: 'String' + required: false + allow_empty: true + default: '' + help: 'Additional arguments for tabix command' scatter_count: type: 'Integer' required: true