Skip to content

Update multivcfanalyzer module#10137

Merged
TCLamnidis merged 21 commits intonf-core:masterfrom
TCLamnidis:update_multivcfanalyzer
Mar 2, 2026
Merged

Update multivcfanalyzer module#10137
TCLamnidis merged 21 commits intonf-core:masterfrom
TCLamnidis:update_multivcfanalyzer

Conversation

@TCLamnidis
Copy link
Copy Markdown
Contributor

@TCLamnidis TCLamnidis commented Feb 23, 2026

This PR:

  • Bumps multivcfanalyzer to the latest version.
  • Swaps to using bgzip for compressing the output snpAlignment.fasta.
  • Adds version topic.
  • adds checking the content of the json output during testing.
  • Updates the nf-test to not use gzip anymore (not needed with latest version).
  • Updates the container links to use new multi-tool container that includes bgzip.

PR checklist

Closes #XXX

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the module conventions in the contribution docs
  • If necessary, include test data in your PR.
  • Remove all TODO statements.
  • Broadcast software version numbers to topic: versions - See version_topics
  • Follow the naming conventions.
  • Follow the parameters requirements.
  • Follow the input/output options guidelines.
  • Add a resource label
  • Use BioConda and BioContainers if possible to fulfil software requirements.
  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
    • For modules:
      • nf-core modules test <MODULE> --profile docker
      • nf-core modules test <MODULE> --profile singularity
      • nf-core modules test <MODULE> --profile conda
    • For subworkflows:
      • nf-core subworkflows test <SUBWORKFLOW> --profile docker
      • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
      • nf-core subworkflows test <SUBWORKFLOW> --profile conda

@TCLamnidis
Copy link
Copy Markdown
Contributor Author

TCLamnidis commented Feb 23, 2026

Linting keeps failing with error

╭─ [✗] 1 Module Test Failed ───────────────────────────────────────────────────╮
│                  ╷                            ╷                              │
│ Module name      │ File path                  │ Test message                 │
│╶─────────────────┼────────────────────────────┼─────────────────────────────╴│
│ multivcfanalyzer │ modules/nf-core/multivcfa… │ wrong_version_output:        │
│                  │                            │ Versions topic output is not │
│                  │                            │ correctly formatted,         │
│                  │                            │ expected tuple               │
│                  │                            │ val("${task.process}"),      │
│                  │                            │ val('<tool>'),               │
│                  │                            │ eval("<version_command>") or │
│                  │                            │ tuple                        │
│                  │                            │ val("${task.process}"),      │
│                  │                            │ val('<tool>'),               │
│                  │                            │ val('<version>')             │
│                  ╵                            ╵                              │
╰──────────────────────────────────────────────────────────────────────────────╯

I do not understand this, since the version pickup of the module is following the examples in the Blog.

https://github.com/nf-core/modules/pull/10137/changes#diff-1b5e1ad4010a7076a06ed9675e4d34e7706bcc8303fdcd4d11b02e5dffad9da2R35-R36

Could this be an issue with nf-core tools?

options "-stub"

setup {
run("GATK_UNIFIEDGENOTYPER", alias: "GATK_UNIFIEDGENOTYPER_STUB") {
Copy link
Copy Markdown
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Why do you need this twice, why not put this outside the first test, and thus you only need to specify it once (although I'm aware you're just updating here)

Copy link
Copy Markdown
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

exactly, because I'm just updating. I stuck with how things were set up originally

Comment thread modules/nf-core/multivcfanalyzer/meta.yml Outdated
Comment thread modules/nf-core/multivcfanalyzer/meta.yml Outdated
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
@TCLamnidis TCLamnidis added this pull request to the merge queue Mar 2, 2026
Merged via the queue into nf-core:master with commit 069d050 Mar 2, 2026
71 checks passed
@TCLamnidis TCLamnidis deleted the update_multivcfanalyzer branch March 2, 2026 13:24
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Projects

None yet

Development

Successfully merging this pull request may close these issues.

2 participants