From 64229d5b8fd9b516e71cc5b849abdb719133cb67 Mon Sep 17 00:00:00 2001 From: Sorel Fitz-Gibbon Date: Mon, 13 Mar 2023 11:20:01 -0700 Subject: [PATCH 01/19] default to empty string for bgzip and tabix extra args --- config/schema.yaml | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/config/schema.yaml b/config/schema.yaml index a462f37e..f5306224 100644 --- a/config/schema.yaml +++ b/config/schema.yaml @@ -66,6 +66,16 @@ 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 + help: 'Additional arguments for bgzip command' +tabix_extra_args: + type: 'String' + required: false + allow_empty: true + help: 'Additional arguments for the FilterMutectCalls command' scatter_count: type: 'Integer' required: true From 2000f575b61d43f6bccb7cb83b003e49039b49ee Mon Sep 17 00:00:00 2001 From: Sorel Fitz-Gibbon Date: Mon, 13 Mar 2023 12:06:54 -0700 Subject: [PATCH 02/19] add default empty string --- config/schema.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/config/schema.yaml b/config/schema.yaml index f5306224..41a2dfb6 100644 --- a/config/schema.yaml +++ b/config/schema.yaml @@ -59,8 +59,6 @@ split_intervals_extra_args: mutect2_extra_args: type: 'String' required: false - allow_empty: true - help: 'Additional arguments for the Mutect2 command' filter_mutect_calls_extra_args: type: 'String' required: false @@ -70,12 +68,14 @@ 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 - help: 'Additional arguments for the FilterMutectCalls command' + default: '' + help: 'Additional arguments for tabix command' scatter_count: type: 'Integer' required: true From 7290c53de91c7c511a6ba7b6676e75b17aabbe19 Mon Sep 17 00:00:00 2001 From: Sorel Fitz-Gibbon Date: Mon, 13 Mar 2023 14:57:27 -0700 Subject: [PATCH 03/19] test 20GB and 2 cpu learnReadOrientation --- config/F32.config | 4 ++-- config/F72.config | 2 +- config/schema.yaml | 2 ++ 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/config/F32.config b/config/F32.config index 64c6b62d..d4e424e8 100644 --- a/config/F32.config +++ b/config/F32.config @@ -60,8 +60,8 @@ process { } } withName: run_LearnReadOrientationModel_GATK { - cpus = 4 - memory = 8.GB + cpus = 2 + memory = 20.GB retry_strategy { memory { strategy = 'exponential' diff --git a/config/F72.config b/config/F72.config index 15301c73..1f61687e 100644 --- a/config/F72.config +++ b/config/F72.config @@ -60,7 +60,7 @@ process { } withName: run_LearnReadOrientationModel_GATK { cpus = 4 - memory = 8.GB + memory = 16.GB retry_strategy { memory { strategy = 'exponential' diff --git a/config/schema.yaml b/config/schema.yaml index 41a2dfb6..ca2ded4c 100644 --- a/config/schema.yaml +++ b/config/schema.yaml @@ -59,6 +59,8 @@ split_intervals_extra_args: mutect2_extra_args: type: 'String' required: false + allow_empty: true + help: 'Additional arguments for the Mutect2 command' filter_mutect_calls_extra_args: type: 'String' required: false From 354af033307bd1ff64de77472fc7b03b2a41f2df Mon Sep 17 00:00:00 2001 From: Sorel Fitz-Gibbon Date: Tue, 14 Mar 2023 13:45:14 -0700 Subject: [PATCH 04/19] set learnReadOrient memory and cpu --- config/F32.config | 2 +- config/F72.config | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/config/F32.config b/config/F32.config index d4e424e8..6e36fb42 100644 --- a/config/F32.config +++ b/config/F32.config @@ -61,7 +61,7 @@ process { } withName: run_LearnReadOrientationModel_GATK { cpus = 2 - memory = 20.GB + memory = 16.GB retry_strategy { memory { strategy = 'exponential' diff --git a/config/F72.config b/config/F72.config index 1f61687e..546a7ab6 100644 --- a/config/F72.config +++ b/config/F72.config @@ -59,7 +59,7 @@ process { } } withName: run_LearnReadOrientationModel_GATK { - cpus = 4 + cpus = 2 memory = 16.GB retry_strategy { memory { From 3c4972f29e59e5d1bdf1dd67e9876edb536ba63c Mon Sep 17 00:00:00 2001 From: Sorel Fitz-Gibbon Date: Tue, 14 Mar 2023 15:06:00 -0700 Subject: [PATCH 05/19] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 50ed9d3e..ab481b4d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,6 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Added - Add NF-test ### Changed +- Update (increase) LearnRaadOrientationModel allocated memory - Update to use `MuSE` v2.0.1 with `MuSE sump` parallelization - Update `MuSE` retry add memory to 48GB - Changed `output_dir` to `output_dir_base` (`methods.config` and `main.nf`) From 1536f83780ff65600120313b8ce689b5682e6ff7 Mon Sep 17 00:00:00 2001 From: Sorel Fitz-Gibbon Date: Wed, 15 Mar 2023 18:40:13 -0700 Subject: [PATCH 06/19] increase mem in F16.config and add bgzip extra args fix to changelog --- CHANGELOG.md | 5 ++++- config/F16.config | 2 +- 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index ab481b4d..38b49494 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,11 +8,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Added - Add NF-test ### Changed -- Update (increase) LearnRaadOrientationModel allocated memory +- Update LearnRaadOrientationModel allocated memory - Update to use `MuSE` v2.0.1 with `MuSE sump` parallelization - 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..93525b97 100644 --- a/config/F16.config +++ b/config/F16.config @@ -61,7 +61,7 @@ process { } withName: run_LearnReadOrientationModel_GATK { cpus = 4 - memory = 8.GB + memory = 16.GB retry_strategy { memory { strategy = 'exponential' From 7fe2c4f5764827e03df81967043a3be79aa47854 Mon Sep 17 00:00:00 2001 From: Sorel Fitz-Gibbon Date: Wed, 15 Mar 2023 18:57:48 -0700 Subject: [PATCH 07/19] cpu update in F16.config for consistency --- config/F16.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/config/F16.config b/config/F16.config index 93525b97..32cd884c 100644 --- a/config/F16.config +++ b/config/F16.config @@ -60,7 +60,7 @@ process { } } withName: run_LearnReadOrientationModel_GATK { - cpus = 4 + cpus = 2 memory = 16.GB retry_strategy { memory { From 87be27e0da0700c8f668009e3299894ad4a87bf6 Mon Sep 17 00:00:00 2001 From: Sorel Fitz-Gibbon Date: Thu, 16 Mar 2023 19:19:00 -0700 Subject: [PATCH 08/19] set learnReadOrient to 1 cpu --- config/F16.config | 2 +- config/F32.config | 2 +- config/F72.config | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/config/F16.config b/config/F16.config index 32cd884c..6abe75b2 100644 --- a/config/F16.config +++ b/config/F16.config @@ -60,7 +60,7 @@ process { } } withName: run_LearnReadOrientationModel_GATK { - cpus = 2 + cpus = 1 memory = 16.GB retry_strategy { memory { diff --git a/config/F32.config b/config/F32.config index 6e36fb42..d8f2a7a8 100644 --- a/config/F32.config +++ b/config/F32.config @@ -60,7 +60,7 @@ process { } } withName: run_LearnReadOrientationModel_GATK { - cpus = 2 + cpus = 1 memory = 16.GB retry_strategy { memory { diff --git a/config/F72.config b/config/F72.config index 546a7ab6..6b0321ae 100644 --- a/config/F72.config +++ b/config/F72.config @@ -59,7 +59,7 @@ process { } } withName: run_LearnReadOrientationModel_GATK { - cpus = 2 + cpus = 1 memory = 16.GB retry_strategy { memory { From 6298b5951cf0451ed63dc3b0512ff67a0e3b3e59 Mon Sep 17 00:00:00 2001 From: Sorel Fitz-Gibbon Date: Mon, 13 Mar 2023 11:20:01 -0700 Subject: [PATCH 09/19] default to empty string for bgzip and tabix extra args --- config/schema.yaml | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/config/schema.yaml b/config/schema.yaml index a462f37e..f5306224 100644 --- a/config/schema.yaml +++ b/config/schema.yaml @@ -66,6 +66,16 @@ 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 + help: 'Additional arguments for bgzip command' +tabix_extra_args: + type: 'String' + required: false + allow_empty: true + help: 'Additional arguments for the FilterMutectCalls command' scatter_count: type: 'Integer' required: true From 22783ade94a608e726eddbda2caa48c76254c874 Mon Sep 17 00:00:00 2001 From: Sorel Fitz-Gibbon Date: Mon, 13 Mar 2023 12:06:54 -0700 Subject: [PATCH 10/19] add default empty string --- config/schema.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/config/schema.yaml b/config/schema.yaml index f5306224..41a2dfb6 100644 --- a/config/schema.yaml +++ b/config/schema.yaml @@ -59,8 +59,6 @@ split_intervals_extra_args: mutect2_extra_args: type: 'String' required: false - allow_empty: true - help: 'Additional arguments for the Mutect2 command' filter_mutect_calls_extra_args: type: 'String' required: false @@ -70,12 +68,14 @@ 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 - help: 'Additional arguments for the FilterMutectCalls command' + default: '' + help: 'Additional arguments for tabix command' scatter_count: type: 'Integer' required: true From c8af5cde7379e0dad7da471f3b11e92fa6a82d24 Mon Sep 17 00:00:00 2001 From: Sorel Fitz-Gibbon Date: Mon, 13 Mar 2023 14:57:27 -0700 Subject: [PATCH 11/19] test 20GB and 2 cpu learnReadOrientation --- config/F32.config | 4 ++-- config/F72.config | 2 +- config/schema.yaml | 2 ++ 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/config/F32.config b/config/F32.config index 64c6b62d..d4e424e8 100644 --- a/config/F32.config +++ b/config/F32.config @@ -60,8 +60,8 @@ process { } } withName: run_LearnReadOrientationModel_GATK { - cpus = 4 - memory = 8.GB + cpus = 2 + memory = 20.GB retry_strategy { memory { strategy = 'exponential' diff --git a/config/F72.config b/config/F72.config index 15301c73..1f61687e 100644 --- a/config/F72.config +++ b/config/F72.config @@ -60,7 +60,7 @@ process { } withName: run_LearnReadOrientationModel_GATK { cpus = 4 - memory = 8.GB + memory = 16.GB retry_strategy { memory { strategy = 'exponential' diff --git a/config/schema.yaml b/config/schema.yaml index 41a2dfb6..ca2ded4c 100644 --- a/config/schema.yaml +++ b/config/schema.yaml @@ -59,6 +59,8 @@ split_intervals_extra_args: mutect2_extra_args: type: 'String' required: false + allow_empty: true + help: 'Additional arguments for the Mutect2 command' filter_mutect_calls_extra_args: type: 'String' required: false From ca533ee2d01fc5663eda55418209fe39ebd3616e Mon Sep 17 00:00:00 2001 From: Sorel Fitz-Gibbon Date: Tue, 14 Mar 2023 13:45:14 -0700 Subject: [PATCH 12/19] set learnReadOrient memory and cpu --- config/F32.config | 2 +- config/F72.config | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/config/F32.config b/config/F32.config index d4e424e8..6e36fb42 100644 --- a/config/F32.config +++ b/config/F32.config @@ -61,7 +61,7 @@ process { } withName: run_LearnReadOrientationModel_GATK { cpus = 2 - memory = 20.GB + memory = 16.GB retry_strategy { memory { strategy = 'exponential' diff --git a/config/F72.config b/config/F72.config index 1f61687e..546a7ab6 100644 --- a/config/F72.config +++ b/config/F72.config @@ -59,7 +59,7 @@ process { } } withName: run_LearnReadOrientationModel_GATK { - cpus = 4 + cpus = 2 memory = 16.GB retry_strategy { memory { From 0dcea53d43e1647301fd31e321752bd6fe7ef074 Mon Sep 17 00:00:00 2001 From: Sorel Fitz-Gibbon Date: Tue, 14 Mar 2023 15:06:00 -0700 Subject: [PATCH 13/19] update changelog --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 86ab1da9..4d5e0ca0 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,6 +9,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Add plantUML action and MuSE flow chart - Add NF-test ### Changed +- Update (increase) LearnRaadOrientationModel allocated memory +- Update to use `MuSE` v2.0.1 with `MuSE sump` parallelization - Update `MuSE` retry add memory to 48GB - Changed `output_dir` to `output_dir_base` (`methods.config` and `main.nf`) From 69d01e42b61d1714d89342d34485147d7a6ab396 Mon Sep 17 00:00:00 2001 From: Sorel Fitz-Gibbon Date: Wed, 15 Mar 2023 18:40:13 -0700 Subject: [PATCH 14/19] increase mem in F16.config and add bgzip extra args fix to changelog --- CHANGELOG.md | 5 ++++- config/F16.config | 2 +- 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 4d5e0ca0..c3e16697 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,11 +9,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Add plantUML action and MuSE flow chart - Add NF-test ### Changed -- Update (increase) LearnRaadOrientationModel allocated memory +- Update LearnRaadOrientationModel allocated memory - Update to use `MuSE` v2.0.1 with `MuSE sump` parallelization - 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..93525b97 100644 --- a/config/F16.config +++ b/config/F16.config @@ -61,7 +61,7 @@ process { } withName: run_LearnReadOrientationModel_GATK { cpus = 4 - memory = 8.GB + memory = 16.GB retry_strategy { memory { strategy = 'exponential' From f64daae60159272e6333f1997d49a8d06f1fc367 Mon Sep 17 00:00:00 2001 From: Sorel Fitz-Gibbon Date: Wed, 15 Mar 2023 18:57:48 -0700 Subject: [PATCH 15/19] cpu update in F16.config for consistency --- config/F16.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/config/F16.config b/config/F16.config index 93525b97..32cd884c 100644 --- a/config/F16.config +++ b/config/F16.config @@ -60,7 +60,7 @@ process { } } withName: run_LearnReadOrientationModel_GATK { - cpus = 4 + cpus = 2 memory = 16.GB retry_strategy { memory { From e68cba7ed266d68f637ea127a4ae7414e757518a Mon Sep 17 00:00:00 2001 From: Sorel Fitz-Gibbon Date: Thu, 16 Mar 2023 19:19:00 -0700 Subject: [PATCH 16/19] set learnReadOrient to 1 cpu --- config/F16.config | 2 +- config/F32.config | 2 +- config/F72.config | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/config/F16.config b/config/F16.config index 32cd884c..6abe75b2 100644 --- a/config/F16.config +++ b/config/F16.config @@ -60,7 +60,7 @@ process { } } withName: run_LearnReadOrientationModel_GATK { - cpus = 2 + cpus = 1 memory = 16.GB retry_strategy { memory { diff --git a/config/F32.config b/config/F32.config index 6e36fb42..d8f2a7a8 100644 --- a/config/F32.config +++ b/config/F32.config @@ -60,7 +60,7 @@ process { } } withName: run_LearnReadOrientationModel_GATK { - cpus = 2 + cpus = 1 memory = 16.GB retry_strategy { memory { diff --git a/config/F72.config b/config/F72.config index 546a7ab6..6b0321ae 100644 --- a/config/F72.config +++ b/config/F72.config @@ -59,7 +59,7 @@ process { } } withName: run_LearnReadOrientationModel_GATK { - cpus = 2 + cpus = 1 memory = 16.GB retry_strategy { memory { From 975e4cd30cfc31df2b51be85868747f501516d44 Mon Sep 17 00:00:00 2001 From: Sorel Fitz-Gibbon Date: Thu, 16 Mar 2023 15:33:04 -0700 Subject: [PATCH 17/19] update changelog --- CHANGELOG.md | 1 + config/default.config | 2 +- metadata.yaml | 2 +- 3 files changed, 3 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index c3e16697..b7e8be44 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Changed - Update LearnRaadOrientationModel allocated memory - Update to use `MuSE` v2.0.1 with `MuSE sump` parallelization +- Update to GATK v4.3.0.0 - Update `MuSE` retry add memory to 48GB - Changed `output_dir` to `output_dir_base` (`methods.config` and `main.nf`) diff --git a/config/default.config b/config/default.config index 7ca6ddfd..c95b933a 100644 --- a/config/default.config +++ b/config/default.config @@ -16,7 +16,7 @@ params { //algorithm version pipeval_version = "2.1.6" samtools_version = "1.16.1" - GATK_version = "4.2.4.1" + GATK_version = "4.3.0.0" somaticsniper_version = "1.0.5.0" bam_readcount_version = "0.8.0" strelka2_version = "2.9.10" diff --git a/metadata.yaml b/metadata.yaml index ea0a60d0..64ea0f8a 100644 --- a/metadata.yaml +++ b/metadata.yaml @@ -5,4 +5,4 @@ Maintainers: ['maotian@mednet.ucla.edu'] Contributors: ['Mao Tian', 'Bugh Caden', 'Helena Winata', 'Yash Patel', 'Sorel Fitz-Gibbon'] Languages: ['Docker', 'Nextflow'] Dependencies: ['Docker', 'Nextflow'] -Tools: ['GATK 4.2.4.1', 'SomaticSniper v1.0.5.0', 'SAMTools v1.16.1', 'Strelka2 v2.9.10', 'Manta v1.6.0', 'MuSE v2.0'] +Tools: ['GATK 4.3.0.0', 'SomaticSniper v1.0.5.0', 'SAMTools v1.16.1', 'Strelka2 v2.9.10', 'Manta v1.6.0', 'MuSE v2.0'] From caab73abccf1190ff8693a1b4329c69936fcf448 Mon Sep 17 00:00:00 2001 From: Sorel Fitz-Gibbon Date: Thu, 16 Mar 2023 16:06:53 -0700 Subject: [PATCH 18/19] update changelog --- CHANGELOG.md | 2 +- config/default.config | 2 +- metadata.yaml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index b7e8be44..bace2890 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,7 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Changed - Update LearnRaadOrientationModel allocated memory - Update to use `MuSE` v2.0.1 with `MuSE sump` parallelization -- Update to GATK v4.3.0.0 +- 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`) diff --git a/config/default.config b/config/default.config index c95b933a..0c4fe09b 100644 --- a/config/default.config +++ b/config/default.config @@ -16,7 +16,7 @@ params { //algorithm version pipeval_version = "2.1.6" samtools_version = "1.16.1" - GATK_version = "4.3.0.0" + GATK_version = "4.4.0.0" somaticsniper_version = "1.0.5.0" bam_readcount_version = "0.8.0" strelka2_version = "2.9.10" diff --git a/metadata.yaml b/metadata.yaml index 64ea0f8a..c82783da 100644 --- a/metadata.yaml +++ b/metadata.yaml @@ -5,4 +5,4 @@ Maintainers: ['maotian@mednet.ucla.edu'] Contributors: ['Mao Tian', 'Bugh Caden', 'Helena Winata', 'Yash Patel', 'Sorel Fitz-Gibbon'] Languages: ['Docker', 'Nextflow'] Dependencies: ['Docker', 'Nextflow'] -Tools: ['GATK 4.3.0.0', 'SomaticSniper v1.0.5.0', 'SAMTools v1.16.1', 'Strelka2 v2.9.10', 'Manta v1.6.0', 'MuSE v2.0'] +Tools: ['GATK 4.4.0.0', 'SomaticSniper v1.0.5.0', 'SAMTools v1.16.1', 'Strelka2 v2.9.10', 'Manta v1.6.0', 'MuSE v2.0'] From 1110d66b0b5ae2fe4cd5b613a5f179492baa6f3e Mon Sep 17 00:00:00 2001 From: Sorel Fitz-Gibbon Date: Mon, 27 Mar 2023 12:51:27 -0700 Subject: [PATCH 19/19] type in changelog --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index bace2890..2e7068d6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -16,7 +16,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Changed `output_dir` to `output_dir_base` (`methods.config` and `main.nf`) ### Fixed -- specify empty string as default for bgzip and tabix extra args +- Specify empty string as default for bgzip and tabix extra args ## [6.0.0-rc.1] - 2023-02-08 ### Changed