Migrate starfusion/build to topics

[mribeirodantas]

PR checklist

Closes #12734

• 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

[mribeirodantas]

Need help here. How to proceed, @LouisLeNezet ?

test Process PARABRICKS_STARFUSION                                                                                                                    │
│                                                                                                                                                       │
│   Test [a429ee07] 'homo_sapiens - single end' FAILED (26.813s)                                                                                        │
│                                                                                                                                                       │
│   Assertion failed:                                                                                                                                   │
│                                                                                                                                                       │
│   1 of 2 assertions failed                                                                                                                            │
│                                                                                                                                                       │
│   Nextflow stdout:                                                                                                                                    │
│                                                                                                                                                       │
│   ERROR ~ Error executing process > 'PARABRICKS_RNAFQ2BAM (test)'                                                                                     │
│                                                                                                                                                       │
│   Caused by:                                                                                                                                          │
│     Process requirement exceeds available memory -- req: 30 GB; avail: 16 GB                                                                          │
│                                                                                                                                                       │
│                                                                                                                                                       │
│   Command executed:                                                                                                                                   │
│                                                                                                                                                       │
│     pbrun \                                                                                                                                           │
│         rna_fq2bam  \                                                                                                                                 │
│         --ref minigenome.fa \                                                                                                                         │
│         --in-se-fq test_starfusion_rnaseq_1.fastq.gz \                                                                                                │
│         --output-dir . \                                                                                                                              │
│         --genome-lib-dir star \                                                                                                                       │
│         --out-bam test.bam \                                                                                                                          │
│         --logfile test.Log.final.out \                                                                                                                │
│         --out-prefix test. \                                                                                                                          │
│         --num-gpus 1 \                                                                                                                                │
│          \                                                                                                                                            │
│         --no-markdups \                                                                                                                               │
│         --num-streams-per-gpu 1 --read-files-command zcat --out-chim-type Junctions --min-chim-segment 15 --x3                                        │
│                                                                                                                                                       │
│   Command exit status:                                    

[LouisLeNezet]

Need help here. How to proceed ?

I guess, you wanted to update this snapshot, but I don't see this error on the github action.
Does it happens locally ?

It seems this particular test use GPU with more memory available.

withName: 'PARABRICKS_RNAFQ2BAM' {
        ext.args = { params.rnafq2bam_args }
        accelerator = [request: 1]
        // The nf-test config caps system memory usage to 4.GB
        // This module requires at least 30 GB to run without error
        // Note: The Github runners run highmem GPU tests on a machine with 31 GB available memory
        // See .github/workflows/nf-test-gpu.yml for exact machine specs
        memory = 30.GB
    }

I would just remove the update on modules/nf-core/parabricks/starfusion/tests/main.nf.test.snap
And see if the github action fails or not.

[LouisLeNezet]

Just a few comments

[mribeirodantas]

Need help here. How to proceed ?

I guess, you wanted to update this snapshot, but I don't see this error on the github action. Does it happens locally ?

It seems this particular test use GPU with more memory available.

withName: 'PARABRICKS_RNAFQ2BAM' {
        ext.args = { params.rnafq2bam_args }
        accelerator = [request: 1]
        // The nf-test config caps system memory usage to 4.GB
        // This module requires at least 30 GB to run without error
        // Note: The Github runners run highmem GPU tests on a machine with 31 GB available memory
        // See .github/workflows/nf-test-gpu.yml for exact machine specs
        memory = 30.GB
    }

I would just remove the update on modules/nf-core/parabricks/starfusion/tests/main.nf.test.snap And see if the github action fails or not.

My point was more like it would be cool if the bot could update the snapshots for us (at least core team) 😆 I know it can for GPU (though not sure if it's working), but it would be good for some specific CPU cases too.

Currently, I can't generate the snapshot for this tool :(

[mribeirodantas]

What I did, @LouisLeNezet

1. Remove tag "starfusion/build" from modules/nf-core/parabricks/starfusion/tests/main.nf.test
2. nf-core modules test starfusion/build --update
3. Add back tag "starfusion/build" in modules/nf-core/parabricks/starfusion/tests/main.nf.test

[LouisLeNezet]

What I did, @LouisLeNezet

1. Remove `tag "starfusion/build"` from `modules/nf-core/parabricks/starfusion/tests/main.nf.test`

2. `nf-core modules test starfusion/build --update`

3. Add back `tag "starfusion/build"` in `modules/nf-core/parabricks/starfusion/tests/main.nf.test`

Personally, for this kind of case, I directly use nf-test test to run only the test I need 😉
You still need to revert the change on the parabricks snapshot.
To do so, the easiest would be to copy paste the whole file from the master branch.

[LouisLeNezet]

My point was more like it would be cool if the bot could update the snapshots for us (at least core team) 😆 I know it can for GPU (though not sure if it's working), but it would be good for some specific CPU cases too.

It might be possible, I'll look into it.

[LouisLeNezet]

Why change from simple touch ?

[mribeirodantas]

I will revert. Just a matter of style from side, my bad.

[mribeirodantas]

Personally, for this kind of case, I directly use nf-test test to run only the test I need 😉

I tried that and failed. I believe there is some magic that nf-core/tools does with staging files. It always works with you?