Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Update error codes for retrying SPAdes #355

Merged
merged 3 commits into from
Nov 25, 2022
Merged

Update error codes for retrying SPAdes #355

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
eb5013d
Add error code 21 to SPAdes retry list
mglubber Nov 17, 2022
4d232d5
Update CHANGELOG.md
mglubber Nov 17, 2022
eff45ab
Update CHANGELOG.md
mglubber Nov 17, 2022
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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`

Expand Down
4 changes: 2 additions & 2 deletions conf/base.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down