Co-authored-by: Krešimir Beštak <86408271+kbestak@users.noreply.github.com>

…-core.yml to fix lint error

rebased on dev

rebased on dev

Add background subtraction

Add our nf-test tests to the GitHub Actions CI

Co-authored-by: Jeremy Muhlich <jmuhlich@bitflood.org>

Use Nextflow file() and toUriString() for cloud storage compatibility

update mcmicro metro image

This will be required for processing pre-stitched images, which will often
include an image pyramid.

This got reverted to the base template version during a template merge.

Update showinf args

Update ro-crate-metadata.json

Remove extraneous code and config lines

Replace switch with if/else in config

Our local modules that use exec: blocks for error checking and other reporting
will fail for stub runs, generally due to trying to parse nonexistent files.
This change skips the affected subworkflows on stub runs. Since there are no
relevant files to parse on a stub run, these steps can safely be skipped.

Fix up local workflows to make a pipeline stub run work

…relude handling

Change exec blocks to independent scripts and improve reporting

Added authors to .nf-core.yml