feat: add vcontact3/run module#12198
Open
JP-Bro wants to merge 13 commits into
Open
Conversation
mashehu
reviewed
Jun 30, 2026
Contributor
There was a problem hiding this comment.
we don't use this file anymore 🙂
mashehu
reviewed
Jun 30, 2026
mashehu
left a comment
mashehu
left a comment
Contributor
There was a problem hiding this comment.
it looks like you started this module an outdated template, so I would recommend to rerun nf-core moduels create with nf-core/tools version 4.0.2. (and then copy over the code)
mashehu
reviewed
Jun 30, 2026
mashehu
left a comment
mashehu
left a comment
Contributor
There was a problem hiding this comment.
looks like you missed the template changes iin the main.nf 🙂
Comment on lines
+30
to
+33
| cat > versions.yml <<-EOF_VERSIONS | ||
| "${task.process}": | ||
| vcontact3: \$( vcontact3 --version 2>&1 | grep -oP 'vcontact3, version \\K[^\\s]+' ) | ||
| EOF_VERSIONS |
Contributor
There was a problem hiding this comment.
use version topics please https://nf-co.re/docs/tutorials/migrate_to_topics/update_modules
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
mashehu
reviewed
Jun 30, 2026
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
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
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
Description
Implements the VCONTACT3/RUN module for viral genome clustering using protein-level homology comparison.
Related Issues
Closes #11569
Module Details
Checklist
Testing
Module created with proper Nextflow DSL2 structure. Ready for integration testing with nf-core CI/CD pipeline.