From 8ef83bda1b2ff08d393009c77616f16cccf25ebb Mon Sep 17 00:00:00 2001 From: Sorel Fitz-Gibbon Date: Mon, 8 Jan 2024 16:00:14 -0800 Subject: [PATCH 1/6] update F16 strelka retry --- config/F16.config | 4 +++- external/pipeline-Nextflow-config | 2 +- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/config/F16.config b/config/F16.config index 9f94f3a0..c976847a 100644 --- a/config/F16.config +++ b/config/F16.config @@ -30,7 +30,9 @@ process { } withName: call_sSNV_Strelka2 { cpus = 16 - memory = 15.GB + memory = 2.GB + errorStrategy = 'retry' + maxRetries = 2 retry_strategy { memory { strategy = 'add' diff --git a/external/pipeline-Nextflow-config b/external/pipeline-Nextflow-config index 27956f3c..1960eaa6 160000 --- a/external/pipeline-Nextflow-config +++ b/external/pipeline-Nextflow-config @@ -1 +1 @@ -Subproject commit 27956f3c2438bf379c14fb5e22bc53ccd9ae8755 +Subproject commit 1960eaa6f390cd9fead6b35b153a26d2bdb7b3fd From 7eb5103918d5248e014f586f717c2d8c3510667f Mon Sep 17 00:00:00 2001 From: Sorel Fitz-Gibbon Date: Wed, 24 Jan 2024 15:09:53 -0800 Subject: [PATCH 2/6] change strelka2 retry --- config/F16.config | 4 +--- config/base.config | 7 ++++++- external/pipeline-Nextflow-config | 2 +- main.nf | 1 - 4 files changed, 8 insertions(+), 6 deletions(-) diff --git a/config/F16.config b/config/F16.config index c976847a..dc62bfab 100644 --- a/config/F16.config +++ b/config/F16.config @@ -31,12 +31,10 @@ process { withName: call_sSNV_Strelka2 { cpus = 16 memory = 2.GB - errorStrategy = 'retry' - maxRetries = 2 retry_strategy { memory { strategy = 'add' - operand = 5.GB + operand = 12.GB } } } diff --git a/config/base.config b/config/base.config index ff3aa126..cfa3ca24 100644 --- a/config/base.config +++ b/config/base.config @@ -1,7 +1,12 @@ process { cpus = { methods.check_limits( 1 * task.attempt, 'cpus' ) } - errorStrategy = { task.exitStatus in [143, 137, 104, 134, 139] ? 'retry' : 'finish' } + commonRetryCodes = [104, 134, 137, 139, 143, 247] // Common out-of-memory error codes + withName: 'call_sSNV_Strelka2' { + ext.retry_codes = [1] // call_sSNV_Strelka2 doesn't differentiate memory errors + } + + errorStrategy = { task.exitStatus in (((task?.ext?.retry_codes) ? task.ext.retry_codes : []) + process.commonRetryCodes) ? 'retry' : 'terminate' } maxRetries = 1 withLabel:process_low { diff --git a/external/pipeline-Nextflow-config b/external/pipeline-Nextflow-config index 1960eaa6..7e10f2c8 160000 --- a/external/pipeline-Nextflow-config +++ b/external/pipeline-Nextflow-config @@ -1 +1 @@ -Subproject commit 1960eaa6f390cd9fead6b35b153a26d2bdb7b3fd +Subproject commit 7e10f2c89cc8c57ecacb7806da88d2adf6759d7d diff --git a/main.nf b/main.nf index ba0a3a3c..24a0b85e 100755 --- a/main.nf +++ b/main.nf @@ -112,7 +112,6 @@ def indexFile(bam_or_vcf) { } } - Channel .from( params.samples_to_process ) .filter{ it.sample_type == 'tumor' } From 2a334da07d28ab8a485e1a9306f95b86bd45f114 Mon Sep 17 00:00:00 2001 From: Sorel Fitz-Gibbon Date: Thu, 25 Jan 2024 13:07:37 -0800 Subject: [PATCH 3/6] update changelog --- CHANGELOG.md | 1 + external/pipeline-Nextflow-config | 2 +- external/pipeline-Nextflow-module | 2 +- 3 files changed, 3 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 469dda0b..3621ffdb 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## [8.0.0-rc.1] - 2023-12-13 ### Changed +- `Strelka2` retry triggered by error code `1` - sample names sanitized for all output - sample names parsed from input BAMs - Update `MuSE` to `v2.0.4` diff --git a/external/pipeline-Nextflow-config b/external/pipeline-Nextflow-config index 7e10f2c8..da8e990e 160000 --- a/external/pipeline-Nextflow-config +++ b/external/pipeline-Nextflow-config @@ -1 +1 @@ -Subproject commit 7e10f2c89cc8c57ecacb7806da88d2adf6759d7d +Subproject commit da8e990e15f136f992a427ed629fe3a2bb78a1ea diff --git a/external/pipeline-Nextflow-module b/external/pipeline-Nextflow-module index b0b2798a..9db08f02 160000 --- a/external/pipeline-Nextflow-module +++ b/external/pipeline-Nextflow-module @@ -1 +1 @@ -Subproject commit b0b2798a5234fad916662fd135272907e7f8e1ab +Subproject commit 9db08f0243ed844ab1f6460dad9a9197cc151605 From 057ad791fb414798a67faf732b3f92aca474e622 Mon Sep 17 00:00:00 2001 From: Sorel Fitz-Gibbon Date: Thu, 25 Jan 2024 13:16:57 -0800 Subject: [PATCH 4/6] adjust retry memory F72 --- config/F72.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/config/F72.config b/config/F72.config index a2770fd5..78605c1d 100644 --- a/config/F72.config +++ b/config/F72.config @@ -52,7 +52,7 @@ process { retry_strategy { memory { strategy = 'add' - operand = 5.GB + operand = 12.GB } } } From 89ae49edf9aaa8b61080afd0db9b92f0f19a2eae Mon Sep 17 00:00:00 2001 From: Sorel Fitz-Gibbon Date: Thu, 25 Jan 2024 13:20:20 -0800 Subject: [PATCH 5/6] fix last commit --- config/F16.config | 8 -------- config/F32.config | 2 +- 2 files changed, 1 insertion(+), 9 deletions(-) diff --git a/config/F16.config b/config/F16.config index 260ed162..45433447 100644 --- a/config/F16.config +++ b/config/F16.config @@ -47,20 +47,12 @@ process { } } withName: call_sSNV_Strelka2 { -<<<<<<< HEAD - cpus = 16 -======= cpus = 6 ->>>>>>> 58309793d38502b8ef6cf1acbd54ca3d217e6d4c memory = 2.GB retry_strategy { memory { strategy = 'add' -<<<<<<< HEAD operand = 12.GB -======= - operand = 4.GB ->>>>>>> 58309793d38502b8ef6cf1acbd54ca3d217e6d4c } } } diff --git a/config/F32.config b/config/F32.config index 678111f2..74a39413 100644 --- a/config/F32.config +++ b/config/F32.config @@ -52,7 +52,7 @@ process { retry_strategy { memory { strategy = 'add' - operand = 5.GB + operand = 12.GB } } } From 30dfed1d9a91b33470404b943066e24d9022df81 Mon Sep 17 00:00:00 2001 From: Sorel Fitz-Gibbon Date: Sun, 28 Jan 2024 19:04:11 -0800 Subject: [PATCH 6/6] strelka config exome false --- test/config/a_mini-strelka2.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/config/a_mini-strelka2.config b/test/config/a_mini-strelka2.config index 907496a8..2d0ef50a 100644 --- a/test/config/a_mini-strelka2.config +++ b/test/config/a_mini-strelka2.config @@ -17,7 +17,7 @@ params { dataset_id = 'TWGSAMIN' // set params.exome to TRUE will add the '--exome' option when running manta and strelka2 // set params.exome to TRUE will add the '-E' option when running MuSE - exome = true + exome = false save_intermediate_files = true // module options