nextflow-io / nextflow-io/nextflow
Add `podman.workDirMountFlags` option to set explicit mount flags for workDir
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- Dominant language
- Groovy
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Description
New feature
Please allow to set mount flags specifically for the working directory, such as :Z, to solve SElinux issues automatically.
Use case
I currently have an SElinux issue when I try to use the podman executor.
Effectively, podman generates the following mount options:
podman run [...] \
-v /scratch/incoming/:/scratch/incoming/ \
-v /s/data/stewardship/GRZ_QC_Workflow/bin:/s/data/stewardship/GRZ_QC_Workflow/bin \
-w /scratch/incoming/<id>/qc/work/58/ad01b84c38eee85faddf6dbd7e95bf \
[...]
I cannot set :Z option on every volume mount as I am not the owner of these folders.
Suggested implementation
While other directories might be read-only, the working directory will always be owned (or at least sufficiently writable) by the executing user.
Therefore, it is a safe assumption that one can always set the :Z mount flag on the working directory.
Could we have an explicit podman.workDirMountFlags option that is set to Z by default?
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
The issue does not name files or tests; start by locating the Podman executor's work-directory mount generation and the existing executor option definitions. Confirm the new option applies only to the working-directory mount, defaults to Z, and add or update coverage for the resulting mount flags.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- groovy
- Domain
- devops
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 42/100