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This reverts commit 15add0e.
Merging template updates (3.0.2)
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 PDF of Metro Map
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Warning Newer version of the nf-core template is available. Your pipeline is using an old version of the nf-core template: 3.5.1. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
This mask is slightly different when generated on the CI runners likely due to some tensorflow floating point issues.
Update modules
Update citations
Switch to image metadata summary for a mesmer mask
Important! Template update for nf-core/tools v3.5.1
11 tasks
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
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First release!