are we okay with dropping a version.yml into a versions topic? this is the guideline for modules with templates, but feels like it would break the topic handling, no?

for modules with templates, should the emit be

versions

or

version_MODULE-NAME

?

and another topic: should we make nf-core linting fail if there are no topic versions in the main.nf? it feels like we are quite good with linting now. Currently it just throws a warning

path "versions.yml"                          , emit: versions_bff, topic: versions

i got this error :

2 Module Tests Failed ───────────────────────────────────────────────────────────────────╮
│             ╷                              ╷                                                  │
│ Module name │ File path                    │ Test message                                     │
│╶────────────┼──────────────────────────────┼─────────────────────────────────────────────────╴│
│ bff         │ modules/nf-core/bff/meta.yml │ correct_meta_outputs: Module meta.yml does not   │
│             │                              │ match main.nf. Outputs should contain:           │
│             │                              │ {'assignment': [['meta',                         │
│             │                              │ '_assignment_bff.csv']], 'metrics': [['meta',    │
│             │                              │ '_metrics_bff.csv']], 'params': [['meta',        │
│             │                              │ '*_params_bff.csv']], 'versions_bff':            │
│             │                              │ ['versions.yml']} Run nf-core modules lint --fix │
│             │                              │ to update the meta.yml file.                     │
│ bff         │ modules/nf-core/bff/main.nf  │ 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>')                                 │
│             ╵                              ╵                                                  │
╰───────────────────────────────────────────────────────────────────────────────────────────────╯

Not sure which account to tag, but @Clint Valentine @Clint Valentine has written this plugin for collating topic versions: https://github.com/fulcrumgenomics/nf-versions Could be useful for the nf-core template perhaps?

Quick question regarding the YAML format for outputs and topics Why is there an extra nested list between the output/topic name and the tuple elements?

output:
  html:
  - - meta:
        type: "map"
        description: "Sample metadata"
    - '*.html':
        type: "file"
        description: "FastQC report"

I would expect it to be like this:

output:
  html:
    - meta:
        type: "map"
        description: "Sample metadata"
    - '*.html':
        type: "file"
        description: "FastQC report"

Hi, For the dragen module we cannot really obtain its version as we need the special hardware to run it. How should we update the module for the topic migration. We also have meta.sex used, should I move it to val(sex) ? https://github.com/nf-core/modules/pull/10853

We are at 73.56% of the modules converted to topics 🎉 (if I properly measured it 😅)

Hopefully we can finish soon! If anyone's available for review: https://github.com/nf-core/modules/pull/11885

Khmer topics migration: https://github.com/nf-core/modules/pull/11887

kallistobustools migration: https://github.com/nf-core/modules/pull/11888

kleborate and kat migration: https://github.com/nf-core/modules/pull/11889

mirtop modules migration: https://github.com/nf-core/modules/pull/11946

metaphlan to topics: https://github.com/nf-core/modules/pull/11947

topic migration of the day ngbits: https://github.com/nf-core/modules/pull/12031

wgsim: https://github.com/nf-core/modules/pull/12017

umitools/group: https://github.com/nf-core/modules/pull/12032

Since nf-test supports topics we can safely start removing the specific versions emits

Might be good to start doing it for new PRs too

Some topics ready for review: - github.com/nf-core/modules/pull/12477 - github.com/nf-core/modules/pull/12478 - github.com/nf-core/modules/pull/12482 - github.com/nf-core/modules/pull/12483 - github.com/nf-core/modules/pull/12484 - github.com/nf-core/modules/pull/12486 - github.com/nf-core/modules/pull/12485

ribotish: https://github.com/nf-core/modules/pull/12475

I've opened a new series of issue for topic migration: github.com/nf-core/modules/issues/12502 There will be only 4 modules left when this one will be closed ! (+ 11 problematic ones)

github.com/nf-core/modules/pull/12515 github.com/nf-core/modules/pull/12517

github.com/nf-core/modules/pull/12507 github.com/nf-core/modules/pull/12516

Here are a few modules convertion ready to be reviewed. Phyloflash need more discussion as the newer conda version block the environment creation. github.com/nf-core/modules/…/LouisLeNezet

In a few days there will be a hackathon. I hope we manage to do a lot of versions to topics 😄

One more ready: github.com/nf-core/modules/pull/12667

repeatmodeler and repeatmasker seem to be failing for me on conda, on the master branch as well. Anyone fancy digging in and trying to figure out how to make them work, else I'll just mark them as not working

List of last 25 modules to be migrated: github.com/nf-core/modules/issues/12884 and the problematic ones here: github.com/nf-core/modules/issues/12792

What should we do about modules that are deprecated and doesn't emit a topic. Should we simply add

topic: versions

to remove them from the list to be migrated ?