From 4ec272284487d40304d009295508d4934aa16db7 Mon Sep 17 00:00:00 2001 From: cmacphillamy Date: Fri, 14 Aug 2026 13:59:04 +0930 Subject: [PATCH 1/2] refactor: Update CSIRO Petrichor queue configuration to 'h24' --- conf/csiro_petrichor.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/csiro_petrichor.config b/conf/csiro_petrichor.config index 4673d104d..dbabb0056 100644 --- a/conf/csiro_petrichor.config +++ b/conf/csiro_petrichor.config @@ -24,5 +24,5 @@ process { module = 'singularity/3.8.7' cache = 'lenient' stageInMode = 'symlink' - queue = 'defq' + queue = 'h24' } From be40c4ed1b836877bc603df4a1030f00d17fe776 Mon Sep 17 00:00:00 2001 From: cmacphillamy Date: Fri, 14 Aug 2026 13:59:11 +0930 Subject: [PATCH 2/2] docs: Update cluster considerations for CSIRO Petrichor queue change to 'h24' --- docs/csiro_petrichor.md | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/docs/csiro_petrichor.md b/docs/csiro_petrichor.md index 343a5e457..2e7231a2b 100644 --- a/docs/csiro_petrichor.md +++ b/docs/csiro_petrichor.md @@ -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