add anvi-gen-contigs-database module#11713
Open
telatin wants to merge 2 commits into
Open
Conversation
famosab
reviewed
Jun 3, 2026
Contributor
famosab
left a comment
famosab
left a comment
There was a problem hiding this comment.
Thank you for your contribution to nf-core! We really appreciate it. I added a few comments to your PR.
| @@ -0,0 +1,39 @@ | |||
| process ANVIO_ANVI_GEN_CONTIGS_DATABASE { | |||
Contributor
There was a problem hiding this comment.
Please stick to the naming scheme described here: module specifications
Contributor
There was a problem hiding this comment.
You can run
nextflow lint -format -sort-declarations -spaces 4 -harshil-alignmenton this file to clean this up nicely.
| --num-threads $task.cpus \\ | ||
| --contigs-fasta $fasta \\ | ||
| --project-name "$prefix" \\ | ||
| --output-db-path ${prefix}.CONTIGS.db \\ |
Contributor
There was a problem hiding this comment.
We want to let the module user decide about the output file naming in their pipeline via ext-prefix. So ideally the output filenames are just ${prefix}.
Comment on lines
+35
to
+38
| { assert process.out.contigs_db.size() == 1 }, | ||
| { assert file(process.out.contigs_db[0][1]).name == "test.CONTIGS.db" }, | ||
| { assert file(process.out.contigs_db[0][1]).length() > 0 }, | ||
| { assert snapshot(process.out.versions_anvio).match("versions") } |
Contributor
There was a problem hiding this comment.
Can we have these asswertions be part of the snapshot?
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
anvi-gen-contigs-databasePR checklist
Closes #11712
topic: versions- See version_topicslabelnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile condanf-core subworkflows test <SUBWORKFLOW> --profile dockernf-core subworkflows test <SUBWORKFLOW> --profile singularitynf-core subworkflows test <SUBWORKFLOW> --profile conda