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Refactor/update csiro petrichor queue #1167

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Refactor/update csiro petrichor queue #1167

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refactor: Update CSIRO Petrichor queue configuration to 'h24'
cmacphillamy Aug 14, 2026
be40c4e
docs: Update cluster considerations for CSIRO Petrichor queue change …
cmacphillamy Aug 14, 2026
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2 changes: 1 addition & 1 deletion conf/csiro_petrichor.config
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Expand Up @@ -24,5 +24,5 @@ process {
module = 'singularity/3.8.7'
cache = 'lenient'
stageInMode = 'symlink'
queue = 'defq'
queue = 'h24'
}
5 changes: 5 additions & 0 deletions docs/csiro_petrichor.md
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Expand Up @@ -19,6 +19,11 @@ module load nextflow singularity

### Cluster considerations

**Note:** August 2026 - The slurm queue was changed from 'defq' to 'h24' as this was causing an issue where Nextflow would begin checking the working directory for `.exitcode` despite the job still running. When Nextflow couldn't find the `.exitcode` file it would then kill the pipeline. Changing the queue to 'h24' seems to have fixed it. See the following issues for more information:

- https://github.com/labsyspharm/mcmicro/issues/169
- https://github.com/nextflow-io/nextflow/issues/5813

Before running an nf-core pipeline you will need to set your project code as a Slurm environment variable:

```bash
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