chore(modules): migrate abricate/run to new version output format

[maxcumminsandfred-lab]

Migrated module to use topic channels for version outputs.

Files changed:

• modules/nf-core/abricate/run/main.nf
• modules/nf-core/abricate/run/meta.yml
• modules/nf-core/abricate/run/tests/main.nf.test.snap

Generated by nfcore-migrate-versions skill (ClawHub pending), OpenClaw 2026.2.24.

Manually curated by @maxlcummins

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

[mashehu]

@nf-core-bot fix linting

[maxcumminsandfred-lab]

The test needs to be updated but I think closing in on finalising this one - about to push something

[mashehu]

tests are fine, the snapshots need to be updated

[maxcumminsandfred-lab]

@nf-core-bot fix linting

[eit-maxlcummins]

Test Process ABRICATE_RUN

  Test [176d7c38] 'bacteroides_fragilis - genome.fa.gz' 
    > Nextflow 25.10.4 is available - Please consider updating your version to it
    > N E X T F L O W  ~  version 25.10.2
    > Launching `/home/runner/_work/modules/modules/.nf-test-176d7c3807ffe61e67729261b5a97250.nf` [extravagant_noether] DSL2 - revision: c28b493c3f
    > [6a/4420f8] Submitted process > ABRICATE_RUN (test)
java.lang.RuntimeException: Different Snapshot:
--- /tmp/expected6200686698709306json   +++ /tmp/found9508482347840373704json  
@@ -1,19 @@                             @@ +1,19 @@                            
   1 [                                     1 [                                 
   2     {                                 2     {                             
   3         "0": [                        3         "0": [                    
-  4             [                                                             
-  5                 "ABRICATE_RUN",                                           
-  6                 "abricate",                                               
-  7                 "1.0.1"                                                   
-  8             ]                                                             
-  9         ],                                                                
- 10         "1": [                                                            
  11             [                         4             [                     
  12                 {                     5                 {                 
  13                     "id": "test",     6                     "id": "test", 
  14                     "single_end":     7                     "single_end": 
false                                   false                                  
  15                 },                    8                 },                
  16                 "test.txt:md5,b48f    9                 "test.txt:md5,b48f
4f5f78982a221038fd9f0a3aa504"           4f5f78982a221038fd9f0a3aa504"          
                                        + 10             ]                     
                                        + 11         ],                        
                                        + 12         "1": [                    
                                        + 13             [                     
                                        + 14                 "ABRICATE_RUN",   
                                        + 15                 "abricate",       
                                        + 16                 "1.0.1"           
  17             ]                        17             ]                     
  18         ],                           18         ],                        
  19         "report": [                  19         "report": [               

    FAILED (29.776s)

Not sure why the order is changing for items in the json locally vs on the runner

[mashehu]

how do you run it locally? what version of nf-test and nextflow?

[maxcumminsandfred-lab]

how do you run it locally? what version of nf-test and nextflow?

Locally on ARM64.

  - nextflow=25.10.4=h2a3209d_0
  - nf-core=3.5.2=pyhdfd78af_0
  - nf-test=0.9.4=h2a3209d_0

Maybe should try GitHub codespaces

[maxcumminsandfred-lab]

Apologies, I was (manually) updating snaps for abritamr/run instead of abricate/run 🫠