Merge pull request #882 from nf-core/maxulysse-patch-1

remove exit strategy for MANTA/STRELKA

CHANGELOG.md

@@ -29,6 +29,7 @@ Bierikjávrre is one of the largest lake in Sarek.
 - [#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`

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' ) }
     }

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",