Open
Conversation
add imaging data remove some unused stuff some updates Update .devcontainer/devcontainer.json Co-authored-by: Alex Valcourt Caron <[email protected]> first try with new container add new files and fix devcontainer fix devcontainer with alex fix main + add nf-test config Update .devcontainer/devcontainer.json Co-authored-by: Alex Valcourt Caron <[email protected]> fix var PATH add subworkflows load_test_data add nextflow.config to be able to play with nf-core modules keep only stub test Update Dockerfile downgrade nf-core Update nextflow.config Fix line ending issues in windows https://code.visualstudio.com/docs/devcontainers/tips-and-tricks#_resolving-git-line-ending-issues-in-containers-resulting-in-many-modified-files Update Dockerfile Fix miniconda version. Due to some python package dependencies python 3.13 does not work yet.
Contributor
Author
|
For the tests that I've ran so far, here's the number of streamlines for the ORIGINAL IMPLEMENTATION of extractor_flow for subject t0003 (it was also giving off several failure/retry errors during runtime) using nextflow 22.10.0 on DSL1: |
Contributor
Author
|
And here's the number of streamlines for the NEW IMPLEMENTATION of extractor_flow for subject t0003 (no errors or warning during runtime) using nextflow 25.04.6 on DSL2: |
EmmaRenauld
reviewed
Jan 27, 2026
EmmaRenauld
left a comment
EmmaRenauld
left a comment
There was a problem hiding this comment.
Just some comments from reading the Readme
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
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
3 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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
Here it is, extractor_flow version 2.0. This is somewhat of a weird pull request as most of the development for this new version was done in a separate repo with an unrelated history (my mistake!). This work was done starting from the nf-neuro-tutorial, which includes commits from that repo, which I tried to squash into the "Initial commit" to avoid polluting the commit history. Since this new version essentially changes the entire repo, it might be easier to review this PR by directly looking at the files instead of trying to compare what changed.
The major changes are the following:
nextflow.configusing each module's given name.Note: Do we want to create a 'release' tag on the original code before merging this PR? Users could then refer to this tag to use the original implementation of the pipeline if need be.