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Set containerOptions for gatkspark in module - #12637

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FriederikeHanssen:container-options
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Set containerOptions for gatkspark in module #12637
FriederikeHanssen wants to merge 1 commit into
nf-core:masterfrom
FriederikeHanssen:container-options

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@FriederikeHanssen

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The spark modules require container options to set the username appropriatly:

The error is because of java not being able to look up the running user and get user information for that. Providing those files from the surrounding system may help

https://nfcore.slack.com/archives/C043FMKUNLB/p1785426088069839

This moves that option from the pipeline into the module per @pinin4fjords request: nf-core/sarek#2257 (comment)

PR checklist

Closes #XXX

  • This comment contains a description of changes (with reason).
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// has no entry for the host UID that docker.runOptions maps it to. Bind-mounting the
// host's /etc/passwd/group (which do have that entry) fixes the native lookup.
containerOptions { workflow.containerEngine in ['singularity', 'apptainer']
? '--bind /etc/passwd:/etc/passwd:ro,/etc/group:/etc/group:ro'

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This shouldn't be needed for singularity/apptainer, it will make sure to provide sensible details.

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