nextflow-io / nextflow-io/nextflow

Add `podman.workDirMountFlags` option to set explicit mount flags for workDir

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stale
Dominant language
Groovy
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Avg merge
2d 11h
Merged PRs (30d)
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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

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. 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

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