From 68792e7ba15592a500a85d9e643c7bd0505244c3 Mon Sep 17 00:00:00 2001 From: Sorel Fitz-Gibbon Date: Mon, 13 May 2024 11:41:46 -0700 Subject: [PATCH 1/7] update resource allocations --- config/F16.config | 16 ++++++++-------- config/F32.config | 12 ++++++------ config/F72.config | 18 +++++++++--------- 3 files changed, 23 insertions(+), 23 deletions(-) diff --git a/config/F16.config b/config/F16.config index 45433447..f8f3a6b3 100644 --- a/config/F16.config +++ b/config/F16.config @@ -22,7 +22,7 @@ process { retry_strategy { memory { strategy = 'add' - operand = 3.GB + operand = 5.GB } } } @@ -32,7 +32,7 @@ process { retry_strategy { memory { strategy = 'add' - operand = 3.GB + operand = 5.GB } } } @@ -42,7 +42,7 @@ process { retry_strategy { memory { strategy = 'add' - operand = 3.GB + operand = 5.GB } } } @@ -58,7 +58,7 @@ process { } withName: call_sSNV_Mutect2 { cpus = 1 - memory = 3.GB + memory = 2.GB retry_strategy { memory { strategy = 'add' @@ -71,8 +71,8 @@ process { memory = 8.GB retry_strategy { memory { - strategy = 'exponential' - operand = 2 + strategy = 'add' + operand = 20.GB } } } @@ -88,11 +88,11 @@ process { } withName: run_sump_MuSE { cpus = 8 - memory = 24.GB + memory = 16.GB retry_strategy { memory { strategy = 'add' - operand = 8.GB + operand = 16.GB } } } diff --git a/config/F32.config b/config/F32.config index 74a39413..57f820b8 100644 --- a/config/F32.config +++ b/config/F32.config @@ -58,21 +58,21 @@ process { } withName: call_sSNV_Mutect2 { cpus = 1 - memory = 3.GB + memory = 2.GB retry_strategy { memory { strategy = 'add' - operand = 3.GB + operand = 2.GB } } } withName: run_LearnReadOrientationModel_GATK { cpus = 1 - memory = 16.GB + memory = 12.GB retry_strategy { memory { - strategy = 'exponential' - operand = 2 + strategy = 'add' + operand = 20.GB } } } @@ -88,7 +88,7 @@ process { } withName: run_sump_MuSE { cpus = 12 - memory = 48.GB + memory = 18.GB retry_strategy { memory { strategy = 'add' diff --git a/config/F72.config b/config/F72.config index 78605c1d..df37d16f 100644 --- a/config/F72.config +++ b/config/F72.config @@ -8,7 +8,7 @@ process { } withName: call_sSNV_SomaticSniper { cpus = 1 - memory = 1.GB + memory = 2.GB retry_strategy { memory { strategy = 'add' @@ -18,11 +18,11 @@ process { } withName: convert_BAM2Pileup_SAMtools { cpus = 1 - memory = 1.GB + memory = 2.GB retry_strategy { memory { strategy = 'add' - operand = 5.GB + operand = 16.GB } } } @@ -68,11 +68,11 @@ process { } withName: run_LearnReadOrientationModel_GATK { cpus = 1 - memory = 16.GB + memory = 12.GB retry_strategy { memory { - strategy = 'exponential' - operand = 2 + strategy = 'add' + operand = 20.GB } } } @@ -87,12 +87,12 @@ process { } } withName: run_sump_MuSE { - cpus = 24 - memory = 80.GB + cpus = 12 + memory = 18.GB retry_strategy { memory { strategy = 'add' - operand = 20.GB + operand = 24.GB } } } From fea2590f8408b213060ee4201564016fe798a6f4 Mon Sep 17 00:00:00 2001 From: Sorel Fitz-Gibbon Date: Mon, 13 May 2024 12:34:14 -0700 Subject: [PATCH 2/7] update changelog --- CHANGELOG.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index f744a43b..adeac510 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -16,6 +16,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Grant explicit permissions for Nextflow configuration test workflow - Update Nextflow configuration test workflows +### Changed +- update resource allocations + ## [8.0.0] - 2024-01-29 ### Changed From 1272a77db020adc835faa318be8f7c383d58cf53 Mon Sep 17 00:00:00 2001 From: Sorel Fitz-Gibbon Date: Mon, 13 May 2024 14:42:39 -0700 Subject: [PATCH 3/7] merge submodule update --- external/pipeline-Nextflow-config | 2 +- external/pipeline-Nextflow-module | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/external/pipeline-Nextflow-config b/external/pipeline-Nextflow-config index af6a606f..3ec71863 160000 --- a/external/pipeline-Nextflow-config +++ b/external/pipeline-Nextflow-config @@ -1 +1 @@ -Subproject commit af6a606f113930e236e7775b259af08baee380e0 +Subproject commit 3ec718630ff1862377815e6c986a8b56cea1115b diff --git a/external/pipeline-Nextflow-module b/external/pipeline-Nextflow-module index 9db08f02..4597ebcf 160000 --- a/external/pipeline-Nextflow-module +++ b/external/pipeline-Nextflow-module @@ -1 +1 @@ -Subproject commit 9db08f0243ed844ab1f6460dad9a9197cc151605 +Subproject commit 4597ebcfa71588a083550123f63aebd5795b7c4d From 80f5403c47d18587a9ade1060efdc649f640e870 Mon Sep 17 00:00:00 2001 From: Sorel Fitz-Gibbon Date: Mon, 13 May 2024 15:55:15 -0700 Subject: [PATCH 4/7] update config submodule --- external/pipeline-Nextflow-config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/external/pipeline-Nextflow-config b/external/pipeline-Nextflow-config index 3ec71863..795384d7 160000 --- a/external/pipeline-Nextflow-config +++ b/external/pipeline-Nextflow-config @@ -1 +1 @@ -Subproject commit 3ec718630ff1862377815e6c986a8b56cea1115b +Subproject commit 795384d7526946ee55328e0f5af3071df22e4dcd From d5bc47bf0d1cccbfae7e01a142342cec93267175 Mon Sep 17 00:00:00 2001 From: Sorel Fitz-Gibbon Date: Mon, 13 May 2024 16:27:24 -0700 Subject: [PATCH 5/7] update pipeline description --- metadata.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/metadata.yaml b/metadata.yaml index 7f7191c9..3f90afb6 100644 --- a/metadata.yaml +++ b/metadata.yaml @@ -1,6 +1,6 @@ --- Category: 'pipeline' -Description: 'A Nextflow pipeline to identify the somatic single nucleotide variants (sSNVs) by comparing a pair of tumor/normal samples.' +Description: 'Nextflow pipeline to identify the somatic single nucleotide variants (sSNVs) by comparing a pair of tumor/normal samples.' Maintainers: [sfitzgibbon@mednet.ucla.edu] Contributors: ['Mao Tian', 'Bugh Caden', 'Helena Winata', 'Yash Patel', 'Sorel Fitz-Gibbon'] Languages: ['Docker', 'Nextflow'] From 6e2cbeb8554c65def2d319348acbc9fbef148811 Mon Sep 17 00:00:00 2001 From: sorelfitzgibbon Date: Mon, 13 May 2024 23:33:20 +0000 Subject: [PATCH 6/7] Autofix Nextflow configuration regression tests --- test/configtest-F16.json | 50 ++++++++++++++++++++-------------------- test/configtest-F32.json | 34 +++++++++++++-------------- 2 files changed, 42 insertions(+), 42 deletions(-) diff --git a/test/configtest-F16.json b/test/configtest-F16.json index 8e364cee..9983ed58 100644 --- a/test/configtest-F16.json +++ b/test/configtest-F16.json @@ -113,7 +113,7 @@ "memory": "6 GB", "retry_strategy": { "memory": { - "operand": "3 GB", + "operand": "5 GB", "strategy": "add" } } @@ -130,7 +130,7 @@ }, "call_sSNV_Mutect2": { "cpus": "1", - "memory": "3 GB", + "memory": "2 GB", "retry_strategy": { "memory": { "operand": "2 GB", @@ -176,7 +176,7 @@ "memory": "1 GB", "retry_strategy": { "memory": { - "operand": "3 GB", + "operand": "5 GB", "strategy": "add" } } @@ -186,7 +186,7 @@ "memory": "1 GB", "retry_strategy": { "memory": { - "operand": "3 GB", + "operand": "5 GB", "strategy": "add" } } @@ -206,17 +206,17 @@ "memory": "8 GB", "retry_strategy": { "memory": { - "operand": "2", - "strategy": "exponential" + "operand": "20 GB", + "strategy": "add" } } }, "run_sump_MuSE": { "cpus": "8", - "memory": "24 GB", + "memory": "16 GB", "retry_strategy": { "memory": { - "operand": "8 GB", + "operand": "16 GB", "strategy": "add" } } @@ -329,9 +329,9 @@ "cpus": "6", "memory": { "1": "6 GB", - "2": "9 GB", - "3": "12 GB", - "closure": "retry_updater(6 GB, add, 3 GB, $task.attempt, memory)" + "2": "11 GB", + "3": "16 GB", + "closure": "retry_updater(6 GB, add, 5 GB, $task.attempt, memory)" } }, "withName:call_sSNV_MuSE": { @@ -346,10 +346,10 @@ "withName:call_sSNV_Mutect2": { "cpus": "1", "memory": { - "1": "3 GB", - "2": "5 GB", - "3": "7 GB", - "closure": "retry_updater(3 GB, add, 2 GB, $task.attempt, memory)" + "1": "2 GB", + "2": "4 GB", + "3": "6 GB", + "closure": "retry_updater(2 GB, add, 2 GB, $task.attempt, memory)" } }, "withName:call_sSNV_SomaticSniper": { @@ -386,18 +386,18 @@ "cpus": "1", "memory": { "1": "1 GB", - "2": "4 GB", - "3": "7 GB", - "closure": "retry_updater(1 GB, add, 3 GB, $task.attempt, memory)" + "2": "6 GB", + "3": "11 GB", + "closure": "retry_updater(1 GB, add, 5 GB, $task.attempt, memory)" } }, "withName:create_IndelCandidate_SAMtools": { "cpus": "1", "memory": { "1": "1 GB", - "2": "4 GB", - "3": "7 GB", - "closure": "retry_updater(1 GB, add, 3 GB, $task.attempt, memory)" + "2": "6 GB", + "3": "11 GB", + "closure": "retry_updater(1 GB, add, 5 GB, $task.attempt, memory)" } }, "withName:plot_VennDiagram_R": { @@ -413,18 +413,18 @@ "cpus": "1", "memory": { "1": "8 GB", - "2": "16 GB", + "2": "28 GB", "3": "31 GB", - "closure": "retry_updater(8 GB, exponential, 2, $task.attempt, memory)" + "closure": "retry_updater(8 GB, add, 20 GB, $task.attempt, memory)" } }, "withName:run_sump_MuSE": { "cpus": "8", "memory": { - "1": "24 GB", + "1": "16 GB", "2": "31 GB", "3": "31 GB", - "closure": "retry_updater(24 GB, add, 8 GB, $task.attempt, memory)" + "closure": "retry_updater(16 GB, add, 16 GB, $task.attempt, memory)" } }, "withName:run_validate_PipeVal": { diff --git a/test/configtest-F32.json b/test/configtest-F32.json index f90b0a31..a4f92a2f 100644 --- a/test/configtest-F32.json +++ b/test/configtest-F32.json @@ -130,10 +130,10 @@ }, "call_sSNV_Mutect2": { "cpus": "1", - "memory": "3 GB", + "memory": "2 GB", "retry_strategy": { "memory": { - "operand": "3 GB", + "operand": "2 GB", "strategy": "add" } } @@ -203,17 +203,17 @@ }, "run_LearnReadOrientationModel_GATK": { "cpus": "1", - "memory": "16 GB", + "memory": "12 GB", "retry_strategy": { "memory": { - "operand": "2", - "strategy": "exponential" + "operand": "20 GB", + "strategy": "add" } } }, "run_sump_MuSE": { "cpus": "12", - "memory": "48 GB", + "memory": "18 GB", "retry_strategy": { "memory": { "operand": "16 GB", @@ -346,10 +346,10 @@ "withName:call_sSNV_Mutect2": { "cpus": "1", "memory": { - "1": "3 GB", - "2": "6 GB", - "3": "9 GB", - "closure": "retry_updater(3 GB, add, 3 GB, $task.attempt, memory)" + "1": "2 GB", + "2": "4 GB", + "3": "6 GB", + "closure": "retry_updater(2 GB, add, 2 GB, $task.attempt, memory)" } }, "withName:call_sSNV_SomaticSniper": { @@ -412,19 +412,19 @@ "withName:run_LearnReadOrientationModel_GATK": { "cpus": "1", "memory": { - "1": "16 GB", + "1": "12 GB", "2": "32 GB", - "3": "64 GB", - "closure": "retry_updater(16 GB, exponential, 2, $task.attempt, memory)" + "3": "52 GB", + "closure": "retry_updater(12 GB, add, 20 GB, $task.attempt, memory)" } }, "withName:run_sump_MuSE": { "cpus": "12", "memory": { - "1": "48 GB", - "2": "64 GB", - "3": "64 GB", - "closure": "retry_updater(48 GB, add, 16 GB, $task.attempt, memory)" + "1": "18 GB", + "2": "34 GB", + "3": "50 GB", + "closure": "retry_updater(18 GB, add, 16 GB, $task.attempt, memory)" } }, "withName:run_validate_PipeVal": { From 1c028933446408e92f4213dcbb4381ee76229cd9 Mon Sep 17 00:00:00 2001 From: Sorel Fitz-Gibbon <3223552+sorelfitzgibbon@users.noreply.github.com> Date: Tue, 14 May 2024 16:53:17 -0700 Subject: [PATCH 7/7] Update CHANGELOG.md Co-authored-by: Yash Patel <86321070+yashpatel6@users.noreply.github.com> --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index adeac510..7c46b640 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -17,7 +17,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Update Nextflow configuration test workflows ### Changed -- update resource allocations +- Update resource allocations ## [8.0.0] - 2024-01-29