Set containerOptions for gatkspark in module - #12637
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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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The spark modules require container options to set the username appropriatly:
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
topic: versions- See version_topicslabelnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile condanf-core subworkflows test <SUBWORKFLOW> --profile dockernf-core subworkflows test <SUBWORKFLOW> --profile singularitynf-core subworkflows test <SUBWORKFLOW> --profile conda