Add apptainer automounts

[sofstam]

This PR adds autoMounts in apptainer.

PR checklist

• This comment contains a description of changes (with reason)
• CHANGELOG.md is updated
• If you've fixed a bug or added code that should be tested, add tests!
• Documentation in docs is updated

[LilyAnderssonLee]

Is it necessary to keep singularity.autoMounts=True when apptainer.autoMounts=true has been set within the apptainer profile? It will take precedence when you use the apptainer profile to run your workflow, right?

[maxulysse]

singularity.autoMounts=True is in the singularity profile, so no issue there

[codecov]

Codecov Report

Merging #2415 (f0ab665) into dev (f71a22a) will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##              dev    #2415   +/-   ##
=======================================
  Coverage   71.07%   71.07%           
=======================================
  Files          87       87           
  Lines        9431     9431           
=======================================
  Hits         6703     6703           
  Misses       2728     2728           

[sofstam]

Will merge :)