refactor: add container-diff

[adthrasher]

Update the digest check for container differences. Since adding the digest check, we've encountered issues and false positives. container-diff provides a deeper (hopefully more robust) check.

This also adds a step to the CI to update containers to point to the branch images for pytest.
It makes developer_scripts/update_container_tags.sh more robust.
It also fixes a small bug in the methylation process_raw_idats script.

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[a-frantz]

The new check is failing for the minfi image. Any idea why that it is? I don't see any changes to it in the "files changed" tab.

[adthrasher]

The new check is failing for the minfi image. Any idea why that it is? I don't see any changes to it in the "files changed" tab.

Yeah, it's correct. This commit (5af65ae#diff-65053fa5a6e57a96b08ea68284f14b607cf161e2efbcfb602ef6f74c97af0c2b) reformatted the R script, but didn't bump the container revision. I'm not convinced that a reformat needs a revision bump, but the check correctly finds that change.

[a-frantz]

oop sorry. You need to update the STAR and minfi container values

[a-frantz]

@adthrasher I think that with the CI changes, we should have green CI now. IDK why the methylation pytest is failing. But aside from that these changes look good.

[adthrasher]

@adthrasher I think that with the CI changes, we should have green CI now. IDK why the methylation pytest is failing. But aside from that these changes look good.

In typical R fashion, the error message is unhelpful.

Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'colnames': object 'CN' not found
Calls: colnames -> .handleSimpleError -> h
Execution halted