Meta maps, parameterization, documentation #26
Merged
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
…ameterization options
Now has unique input names
It's required now, moved to another section and its allowed values is updated
In higher-level processing
was previously not used at all
This would help to discard data early on that is outside of the area of interest The change to the snapshot is necessary because in preprocessing for the small test dataset, we now have a tile that is being cropped with the new AOI and then the cloud cover in the remaining image is higher than the allowed threshold. This prompts FORCE to discard the output for that tile.
This is done to enable running the pipeline with minimal parameters, because SMA would require the optional parameter params.endmember to be provided.
charles-plessy
approved these changes
Jun 2, 2025
charles-plessy
left a comment
There was a problem hiding this comment.
Looks good to me! Now I understand what you meant when you said you are not bioinformatician.
I have one minor question on the pipeline's metro map diagram. Why is the Endmember path curved in the opposite direction to the others? It gives me the impression that it is an input, although the black bar says it is an output.
docs/usage.md
Outdated
| ### Datacube | ||
|
|
||
| The datacube definition stores information about the projection and reference grid of the generated datacube. | ||
| For details see the [FORCE main paper](https://www.mdpi.com/2072-4292/11/9/1124) and the [datacube tutorila](https://force-eo.readthedocs.io/en/latest/howto/datacube.html). |
Collaborator
Author
|
@charles-plessy thanks for the review. |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
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.
General
This PR includes changes aimed at further aligning this Earth Observation pipeline with nf-core.
The requirements for running the pipeline were eased so that fewer inputs are required and defaults values are chosen in a more sensible way.
Meta maps
Meta maps are introduced, albeit in a somewhat experimental state.
The primary reason for this is to push our local modules closer to actual nf-core/modules.
Parameterization
Most changes give users new ways to configure the pipeline by exposing many tool parameters for local modules.
This also involves integrating parameter file generation for the underlying FORCE tool in the corresponding processes, which was done in a separate process before.
Documentation
All of these changes prompted an extensive rework of all documentation files.
PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).