ICR Alma #845
ICR Alma #845
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Overall looks good @rachelicr ! Some recommendations/suggestions below
conf/icr_alma.config
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| process { | ||
| queue="compute" | ||
| executor = "SLURM" |
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| executor = "SLURM" | |
| executor = "slurm" |
conf/icr_alma.config
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| shell = ['/bin/bash', '-euo', 'pipefail'] | ||
| // memory errors which should be retried. otherwise error out | ||
| errorStrategy = { task.exitStatus in [143,137,104,134,139,140,247] ? 'retry' : 'finish' } |
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You shouldn't need to define this here, both are already predefined in each pipeline. Particularly the error strategy one some pipelines may have extended this list, and you don't want to override those
docs/icr_alma.md
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| Singularity is installed on the compute nodes of Alma, but not the login nodes. There is no module for Singularity. | ||
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| All of the intermediate files required to run the pipeline will be stored in the `work/` directory. It is recommended to delete this directory after the pipeline has finished successfully because it can get quite large. |
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If you want this to be cleaned up automatically on a successful run, you can specify cleanup = true . If a pipeline fails, the cleanup doesn't occur even if this is set to true to allow you to debug the run
docs/icr_alma.md
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| #SBATCH --time=1:00:00 | ||
| #SBATCH --mem-per-cpu=4000 | ||
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| nextflow run nf-core/sarek -profile singularity,test -profile icr_alma |
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| nextflow run nf-core/sarek -profile singularity,test -profile icr_alma | |
| nextflow run nf-core/sarek -profile icr_alma,test --outdir ./results |
conf/icr_alma.config
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| maxErrors = '-1' | ||
| clusterOptions = '--mem-per-cpu=8000' | ||
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| max_memory = '256.GB' |
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Nax_menory seems to be duplicated now, and I just released the max_ parameters are in the wrong place - they should be in params
Resourcelimits are fine where they are though @rachelicr
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conf/icr_alma.config
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| maxErrors = '-1' | ||
| clusterOptions = '--mem-per-cpu=8000' | ||
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| max_memory = '256.GB' |
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See my older comment you did not resolve previously in regards to the position of the |
accepting review suggestion - thanks. Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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Lgtm! |
name: New Config
about: A new cluster config
Please follow these steps before submitting your PR:
[WIP]in its titlemasterbranchSteps for adding a new config profile:
conf/directorydocs/directorynfcore_custom.configfile in the top-level directoryREADME.mdfile in the top-level directoryprofile:scope in.github/workflows/main.yml.github/CODEOWNERS(**/<custom-profile>** @<github-username>)