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ljelonek-public
podman-on-slurm
Commits
53a60f06
Commit
53a60f06
authored
1 month ago
by
Lukas Jelonek
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Add minimal nextflow example
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nextflow/README.md
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nextflow/README.md
nextflow/main.nf
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nextflow/nextflow.config
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# A minimal nextflow example that uses podman on the bcf slurm cluster.
## Assumptions
*
You work from
`cli`
*
You have the system proxy variables set in your current terminal session
## Run
```
nextflow run main.nf
```
If you observe errors, please notify us with a detailed error report, so that
we can improve the configuration over time. This example won't cover all use-
cases at the moment, so it may happen that your workflow won't run with the
provided configuration. In that case contact us, so that we can try to find
solutions for your specific problem and integrate these into this example.
## Notes
Feel free to use the provided
`nextflow.config`
as a starter for your own
workflows.
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process
Hello
{
output:
path
(
"hi.txt"
)
script:
"""
echo "Hoho" > hi.txt
"""
}
workflow
{
Hello
()
}
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nextflow/nextflow.config
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process
{
container
=
'ubuntu:24.10'
executor
=
'slurm'
clusterOptions
=
"--export=http_proxy,https_proxy,ftp_proxy"
queue
=
'bcf'
}
podman
{
enabled
=
true
}
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