Merge pull request #355 from mglubber/dev

Update error codes for retrying SPAdes
nf-core · Nov 25, 2022 · 07b4985 · 07b4985
2 parents 0bd574e + eff45ab
commit 07b4985
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -16,6 +16,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#345](https://github.com/nf-core/mag/pull/345) - Bowtie2 mode changed to global alignment for ancient DNA mode (`--very-sensitive` mode) to prevent soft clipping at the end of reads when running in local mode.
 - [#349](https://github.com/nf-core/mag/pull/349) - Add a warning that pipeline will reset minimum contig size to 1500 specifically MetaBAT2 process, if a user supplies below this threshold.
 - [#352](https://github.com/nf-core/mag/pull/352) - Escape the case in the BUSCO module that BUSCO can just detect a root lineage but is not able to find any marker genes
+- [#355](https://github.com/nf-core/mag/pull/355) - Include error code 21 for retrying with higher memory for SPAdes and hybridSPAdes
 
 ### `Dependencies`
 

diff --git a/conf/base.config b/conf/base.config
@@ -135,14 +135,14 @@ process {
         cpus          = { check_spades_cpus (10, task.attempt) }
         memory        = { check_max (64.GB * (2**(task.attempt-1)), 'memory' ) }
         time          = { check_max (24.h  * (2**(task.attempt-1)), 'time'   ) }
-        errorStrategy = { task.exitStatus in [143,137,1] ? 'retry' : 'finish' }
+        errorStrategy = { task.exitStatus in [143,137,21,1] ? 'retry' : 'finish' }
         maxRetries    = 5
     }
     withName: SPADESHYBRID {
         cpus          = { check_spadeshybrid_cpus (10, task.attempt) }
         memory        = { check_max (64.GB * (2**(task.attempt-1)), 'memory' ) }
         time          = { check_max (24.h  * (2**(task.attempt-1)), 'time'   ) }
-        errorStrategy = { task.exitStatus in [143,137,1] ? 'retry' : 'finish' }
+        errorStrategy = { task.exitStatus in [143,137,21,1] ? 'retry' : 'finish' }
         maxRetries    = 5
     }
     //returns exit code 247 when running out of memory