Add optional publishDir for bioformats2ometiff converted images #32
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Co-authored-by: adamjtaylor <[email protected]>
adamjtaylor
approved these changes
Jan 15, 2026
Copilot
AI
changed the title
[WIP] Add optional save for converted images in bioformats2ometiff
Add optional publishDir for bioformats2ometiff converted images
Jan 15, 2026
adamjtaylor
approved these changes
Jan 15, 2026
There was a problem hiding this comment.
Pull request overview
This PR adds an optional parameter to save converted OME-TIFF files from the bioformats2ometiff process. Currently, these intermediate files are not published and are lost after the pipeline completes. The new --save_ometiff parameter (default: false) allows users to optionally save these files to an ometiff subdirectory within each sample's output directory.
Changes:
- Added
save_ometiffboolean parameter to control publishing of converted OME-TIFF files - Configured publishDir directive in bioformats2ometiff module with conditional publishing
- Updated documentation to reflect the new optional output directory structure
Reviewed changes
Copilot reviewed 4 out of 4 changed files in this pull request and generated 3 comments.
| File | Description |
|---|---|
| main.nf | Added save_ometiff parameter with default value of false |
| modules/bioformats2ometiff.nf | Added conditional publishDir directive to optionally save OME-TIFF files |
| nextflow_schema.json | Added save_ometiff parameter definition and fixed schema reference from non-existent "parameters" to "input_output_options" |
| README.md | Documented the new optional ometiff output directory and the save_ometiff parameter |
💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.
Co-authored-by: Copilot <[email protected]>
Co-authored-by: adamjtaylor <[email protected]>
adamjtaylor
requested review from
aditigopalan
and removed request for
thomasyu888
adamjtaylor
reviewed
Jan 15, 2026
Comment on lines
28
to
70
| "miniatue_options": { | ||
| "miniature_options": { | ||
| "title": "Miniature options", | ||
| "type": "object", | ||
| "fa_icon": "fas fa-palette", | ||
| "description": "Define HTAN Artist pipeline parameters.", | ||
| "properties": { | ||
| "remove_bg": { | ||
| "type": "boolean", | ||
| "description": "Remove non-tissue background", | ||
| "default": true | ||
| }, | ||
| "level": { | ||
| "type": "integer", | ||
| "description": "The pyramid level used in thumbnauls, Default: -1 (smallest)", | ||
| "default": -1 | ||
| }, | ||
| "dimred": { | ||
| "type": "string", | ||
| "description": "The dimensionality reduction method used", | ||
| "default": "umap", | ||
| "enum": ["umap", "tsne", "pca"] | ||
| }, | ||
| "colormap": { | ||
| "type": "string", | ||
| "description": "The colormap used. Ensure colormap is compatiable with `n_components` selected ", | ||
| "enum": ["UCIE", "LAB", "RGB", "BREMM", "SCHUMANN", "STEIGER", "TEULING2", "ZIEGLER","CUBEDIAGONAL"], | ||
| "default": "UCIE" | ||
| }, | ||
| "n_components": { | ||
| "type": "integer", | ||
| "description": "", | ||
| "default": 3, | ||
| "enum": [2,3] | ||
| } | ||
| } | ||
| } | ||
| }, | ||
| "allOf": [ | ||
| { | ||
| "$ref": "#/definitions/parameters" | ||
| "$ref": "#/definitions/input_output_options" | ||
| }, | ||
| { | ||
| "$ref": "#/definitions/miniature_options" | ||
| } | ||
| ] | ||
| } |
Collaborator
Author
aditigopalan
approved these changes
Jan 15, 2026
Collaborator
aditigopalan
left a comment
aditigopalan
left a comment
There was a problem hiding this comment.
lgtm pending: can we pin the java version in .docker/Dockerfile.devenv
FROM openjdk:17-slim
Co-authored-by: adamjtaylor <[email protected]>
Collaborator
|
Thanks @aditigopalan. Issue made re pinning java version |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Implementation Plan for Optional OME-TIFF Saving
save_ometiffparameter to main.nf (default: false)publishDirdirective to bioformats2ometiff.nf module with conditional publishingOriginal prompt
💬 We'd love your input! Share your thoughts on Copilot coding agent in our 2 minute survey.