diff --git a/CHANGELOG.md b/CHANGELOG.md index 4c51091be..d0d9e23ca 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -18,6 +18,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. - [#673](https://github.com/nf-core/eager/pull/673) Fix Kraken database loading when loading from directory instead of compressed file. - [#688](https://github.com/nf-core/eager/issues/668) - Allow pipeline to complete, even if Qualimap crashes due to an empty or corrupt BAM file for one sample/library - [#683](https://github.com/nf-core/eager/pull/683) - Sets `--igenomes_ignore` to true by default, as rarely used by users currently and makes resolving configs less complex. +- Added exit code `140` to re-tryable exit code list to account for certain scheduler wall-time limit fails. ### `Dependencies` diff --git a/conf/base.config b/conf/base.config index cf40abc17..5cfa9ba3e 100644 --- a/conf/base.config +++ b/conf/base.config @@ -14,7 +14,7 @@ process { memory = { check_max( 7.GB * task.attempt, 'memory' ) } time = { check_max( 24.h * task.attempt, 'time' ) } - errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' } + errorStrategy = { task.exitStatus in [143,137,104,134,139, 140] ? 'retry' : 'finish' } maxRetries = 3 maxErrors = '-1' @@ -74,7 +74,7 @@ process { } withName:qualimap{ - errorStrategy = { task.exitStatus in [1,143,137,104,134,139] ? 'retry' : task.exitStatus in [255] ? 'ignore' : 'finish' } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139, 140] ? 'retry' : task.exitStatus in [255] ? 'ignore' : 'finish' } } withName:preseq { @@ -82,26 +82,26 @@ process { } withName:damageprofiler { - errorStrategy = { task.exitStatus in [1,143,137,104,134,139] ? 'retry' : 'finish' } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139, 140] ? 'retry' : 'finish' } } // Add 1 retry for certain java tools as not enough heap space java errors gives exit code 1 withName: dedup { - errorStrategy = { task.exitStatus in [1,143,137,104,134,139] ? 'retry' : 'finish' } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139, 140] ? 'retry' : 'finish' } } withName: markduplicates { - errorStrategy = { task.exitStatus in [143,137] ? 'retry' : 'finish' } + errorStrategy = { task.exitStatus in [143,137, 140] ? 'retry' : 'finish' } } // Add 1 retry as not enough heapspace java error gives exit code 1 withName: malt { - errorStrategy = { task.exitStatus in [1,143,137,104,134,139] ? 'retry' : 'finish' } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139, 140] ? 'retry' : 'finish' } } // other process specific exit statuses withName: nuclear_contamination { - errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'ignore' : 'retry' } + errorStrategy = { task.exitStatus in [143,137,104,134,139, 140] ? 'ignore' : 'retry' } } }