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Add docker.runOptions to avoid memory swap error #351

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Jun 28, 2019
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Add docker.runOptions to avoid memory swap error #351

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5 changes: 5 additions & 0 deletions nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config
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Expand Up @@ -58,6 +58,11 @@ profiles {
test { includeConfig 'conf/test.config' }
}

// Avoid this error:
// WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
// Thanks to: https://github.com/alesssia/YAMP/wiki/How-to-use-Docker
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Suggested change
// Thanks to: https://github.com/alesssia/YAMP/wiki/How-to-use-Docker
// Thanks to: https://github.com/alesssia/YAMP/wiki/How-to-use-Docker
// Testing this in nf-core after discussion here https://github.com/nf-core/tools/pull/351, once this is established and works well, nextflow might implement this behavior as new default.

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Could you add this in @olgabot? That should be enough to be able to trace things back once they're in the template.

docker.runOptions = '-u $(id -u):$(id -g)'
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Shouldn't it be -u \$(id -u):\$(id -g)?
cf: https://github.com/nf-core/sarek/blob/10eff4e8ff71e672d73a3bf4aa43a3693342bfb2/nextflow.config#L63

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Not sure that is required - the '...' should be enough if it's in nextflow.config right?

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sorry, I didn't understood what you meant ;-)

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I mean I'm not sure whether we need to escape the $ with a \$ here as they are inside a '...' single quotes block :)

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Aaaah, now I understand.
I'm pretty sure I copied that from someone else (probably Paolo) at some point.
I'm guessing the double quotes render the escaping the $ a necessity

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Then we need to address this as well - I was looking for another place where this is used but couldn't find it. Wouldn't fixOwnership as listed here do the same? https://www.nextflow.io/docs/latest/config.html#config-docker


// Load igenomes.config if required
if(!params.igenomesIgnore){
includeConfig 'conf/igenomes.config'
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