add option --ignore-stains

[akhanf]

for dealing with inconsistent stains across subjects, can use this to ignore those
that are not common to all subjects

[Copilot]

Pull request overview

Adds a new workflow configuration/CLI option to tolerate inconsistent staining across subjects by allowing specific stains to be ignored when determining the dataset’s stain set, improving robustness of multi-subject runs when extra channels appear only in some subjects.

Changes:

• Add ignore_stains CLI/config option and pass it into stain discovery in the main Snakefile.
• Update get_stains_all_subjects() to optionally filter out ignored stains before enforcing cross-subject consistency.
• Clarify help text for registration/segmentation downsampling level options.

Reviewed changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated 2 comments.

File	Description
spimquant/workflow/Snakefile	Passes configured ignored stains into stain discovery when sample_staining isn’t provided.
spimquant/workflow/rules/common.smk	Extends stain-consistency logic to support filtering out ignored stains before comparing subjects.
spimquant/config/snakebids.yml	Exposes new CLI option for ignored stains and refines downsampling help strings.