feat: addition of vembrane sort module #9294
Open
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
mkatsanto
moved this from To do
to Ready for review
in Hackathon Barcelona October 2025
famosab
reviewed
Oct 29, 2025
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out).match() } |
There was a problem hiding this comment.
Suggested change
| { assert snapshot(process.out).match() } | |
| { assert snapshot( | |
| process.out, | |
| path(process.out.versions[0]).yaml | |
| ).match() } |
famosab
reviewed
Oct 29, 2025
There was a problem hiding this comment.
This is added in the other PR right?, can you remove it here? :)
There was a problem hiding this comment.
Sorry, what I meant: can you please do one PR per module :) meaning one seperate one for vembrane/table?
famosab
reviewed
Oct 29, 2025
There was a problem hiding this comment.
Can you run
nextflow lint -format -sort-declarations -spaces 4 -harshil-alignment modules/nf-core/vembrane/sort/main.nf
please? :)
|
|
Seems like gzipped vcfs are not allowed. I would suggest to open an issue over at the vembrane repo to request that and remove it from the module for now :) You can link to the PR in the issue you open :) |
famosab
reviewed
Oct 29, 2025
Comment on lines
89
to
114
| test("homo_sapiens - [vcf] - vcf - compressed_output") { | ||
|
|
||
| config "./nextflow.config" | ||
|
|
||
| when { | ||
| params { | ||
| vembrane_args = '--output-fmt vcf.gz' | ||
| } | ||
| process { | ||
| """ | ||
| input[0] = [ | ||
| [ id:'test_gz' ], // meta map | ||
| file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/test.rnaseq.vcf', checkIfExists: true) | ||
| ] | ||
| input[1] = 'QUAL' | ||
| """ | ||
| } | ||
| } | ||
|
|
||
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out).match() } | ||
| ) | ||
| } | ||
| } |
There was a problem hiding this comment.
Suggested change
| test("homo_sapiens - [vcf] - vcf - compressed_output") { | |
| config "./nextflow.config" | |
| when { | |
| params { | |
| vembrane_args = '--output-fmt vcf.gz' | |
| } | |
| process { | |
| """ | |
| input[0] = [ | |
| [ id:'test_gz' ], // meta map | |
| file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/test.rnaseq.vcf', checkIfExists: true) | |
| ] | |
| input[1] = 'QUAL' | |
| """ | |
| } | |
| } | |
| then { | |
| assertAll( | |
| { assert process.success }, | |
| { assert snapshot(process.out).match() } | |
| ) | |
| } | |
| } |
| - "*.vcf*": | ||
| type: file | ||
| description: Sorted VCF file (can be compressed) | ||
| pattern: "*.{vcf,vcf.gz}" |
There was a problem hiding this comment.
Suggested change
| pattern: "*.{vcf,vcf.gz}" | |
| pattern: "*.{vcf,bcf}" |
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.
PR checklist
Fixes #9265
Addition of the vembrane sort module https://github.com/vembrane/vembrane
versions.ymlfile.labelnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile conda