BUG: permissions of falco output

[DriesSchaumont]

Description

Falco, by default, creates the output folder in mode 700 only. See https://github.com/smithlabcode/falco/blob/3e4f0ad4bee3fa84280c179cc4320bf103c59262/src/falco.cpp#L635

This means that using this component with docker creates files as root, which are not usable by the user and causes problems when publishing. There are two solutions for this:

• in the script, use chmod g+rx,o+rx on the output folder
• use docker.fixOwnership = true. It think this option is preferred because it just changes the owner of the files, not the mode and the fix is only applied when using docker.

Why is this not a problem for other components? The behavior occurs when:

1. There is an output argument of type file
2. This output will be created by the script of the component and its a directory.
3. The created directory missing read and execute permissions for 'others'.

Most other components create files, for which the permissions are based on the umask. The umask is by default 022, so most of the times the files are created with permissions 0644. This includes read permissions for groups and others.

Issue ticket number

Closes #xxxx

Checklist before requesting a review

• I have performed a self-review of my code

• Conforms to the Contributing guidelines

• Proposed changes are described in the CHANGELOG.md

• I have tested my code with viash ns test --parallel -q <name or namespace>

• Check the correct box. Does this PR contain:

  • Breaking changes
  • New functionality
  • Major changes
  • Minor changes
  • Documentation
  • Bug fixes

[DriesSchaumont]

Ah, the proposed solution to add fixOwnership to only this component does not work when this component is used as a dependency. The fixOwnership gets added to the nextflow.config for this component, but this config file that needs to be added manually with each run

[DriesSchaumont]

Closing in favour of viash-io/viash#727