diff --git a/CHANGELOG.md b/CHANGELOG.md index 906839b0d2..3bf5065196 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -27,6 +27,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#860](https://github.com/nf-core/sarek/pull/860) - Replace local subworkflow with nf-core version - `vcf_annotate_snpeff` - [#865](https://github.com/nf-core/sarek/pull/865) - Replace local subworkflow with nf-core version - `vcf_annotate_ensemblvep` - [#874](https://github.com/nf-core/sarek/pull/874) - Update all modules +- [#882](https://github.com/nf-core/sarek/pull/882) - Remove exit strategy for `Manta`/`Strelka` - [#890](https://github.com/nf-core/sarek/pull/890) - Sync `TEMPLATE` with `tools` `2.7.1` - [#896](https://github.com/nf-core/sarek/pull/896) - Code refactoring - [#898](https://github.com/nf-core/sarek/pull/898) - Nextflow minimal version is now `22.10.1` diff --git a/conf/base.config b/conf/base.config index 1945ad9aa9..db1175874f 100644 --- a/conf/base.config +++ b/conf/base.config @@ -83,7 +83,6 @@ process { memory = { check_max( 4.GB * task.attempt, 'memory' ) } } withName:'STRELKA.*|MANTA.*' { - errorStrategy = { task.exitStatus in [143,137,104,134,139,140,247,1] ? 'retry' : 'finish' } cpus = { check_max( 10 * task.attempt, 'cpus' ) } memory = { check_max( 8.GB * task.attempt, 'memory' ) } } diff --git a/modules.json b/modules.json index c3edc56893..8dbf98e633 100644 --- a/modules.json +++ b/modules.json @@ -288,17 +288,17 @@ }, "manta/germline": { "branch": "master", - "git_sha": "0460d316170f75f323111b4a2c0a2989f0c32013", + "git_sha": "80dbd95c558a0ebb2123d95f50c093a7f714a0d7", "installed_by": ["modules"] }, "manta/somatic": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "80dbd95c558a0ebb2123d95f50c093a7f714a0d7", "installed_by": ["modules"] }, "manta/tumoronly": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "80dbd95c558a0ebb2123d95f50c093a7f714a0d7", "installed_by": ["modules"] }, "mosdepth": { @@ -379,16 +379,16 @@ "snpeff/snpeff": { "branch": "master", "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", - "installed_by": ["modules", "vcf_annotate_snpeff"] + "installed_by": ["vcf_annotate_snpeff", "modules"] }, "strelka/germline": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "80dbd95c558a0ebb2123d95f50c093a7f714a0d7", "installed_by": ["modules"] }, "strelka/somatic": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "80dbd95c558a0ebb2123d95f50c093a7f714a0d7", "installed_by": ["modules"] }, "svdb/merge": { @@ -399,7 +399,7 @@ "tabix/bgziptabix": { "branch": "master", "git_sha": "01b3b2509d76625b6d6cd613b349fb4777712a15", - "installed_by": ["modules", "vcf_annotate_snpeff"] + "installed_by": ["vcf_annotate_snpeff", "modules"] }, "tabix/tabix": { "branch": "master", diff --git a/modules/nf-core/manta/germline/main.nf b/modules/nf-core/manta/germline/main.nf index 8f785fe025..e052b7c9f0 100644 --- a/modules/nf-core/manta/germline/main.nf +++ b/modules/nf-core/manta/germline/main.nf @@ -1,6 +1,7 @@ process MANTA_GERMLINE { tag "$meta.id" label 'process_medium' + label 'error_retry' conda "bioconda::manta=1.6.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? diff --git a/modules/nf-core/manta/somatic/main.nf b/modules/nf-core/manta/somatic/main.nf index f164ec0143..817abcb523 100644 --- a/modules/nf-core/manta/somatic/main.nf +++ b/modules/nf-core/manta/somatic/main.nf @@ -1,6 +1,7 @@ process MANTA_SOMATIC { tag "$meta.id" label 'process_medium' + label 'error_retry' conda "bioconda::manta=1.6.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? diff --git a/modules/nf-core/manta/tumoronly/main.nf b/modules/nf-core/manta/tumoronly/main.nf index 55d28e91ad..3d8b8b9c84 100644 --- a/modules/nf-core/manta/tumoronly/main.nf +++ b/modules/nf-core/manta/tumoronly/main.nf @@ -1,6 +1,7 @@ process MANTA_TUMORONLY { tag "$meta.id" label 'process_medium' + label 'error_retry' conda "bioconda::manta=1.6.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? diff --git a/modules/nf-core/strelka/germline/main.nf b/modules/nf-core/strelka/germline/main.nf index 9acbb67f55..74712df16b 100644 --- a/modules/nf-core/strelka/germline/main.nf +++ b/modules/nf-core/strelka/germline/main.nf @@ -1,6 +1,7 @@ process STRELKA_GERMLINE { tag "$meta.id" label 'process_medium' + label 'error_retry' conda "bioconda::strelka=2.9.10" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? diff --git a/modules/nf-core/strelka/somatic/main.nf b/modules/nf-core/strelka/somatic/main.nf index dc099d4c3c..17d700c136 100644 --- a/modules/nf-core/strelka/somatic/main.nf +++ b/modules/nf-core/strelka/somatic/main.nf @@ -1,6 +1,7 @@ process STRELKA_SOMATIC { tag "$meta.id" label 'process_medium' + label 'error_retry' conda "bioconda::strelka=2.9.10" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?