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Add STIMULUS/CHECKTORCHMODEL #6898

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Add STIMULUS/CHECKTORCHMODEL #6898

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itrujnara
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@itrujnara itrujnara commented Oct 29, 2024 •
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Closes #6872
Closes nf-core/deepmodeloptim#197

PR checklist

  • 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.
  • Emit the versions.yml file.
  • 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

@itrujnara
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The nf-test fails because the current version of the Python script expects a JSON and the test data is YAML. It will be fixed soon.

vagkaratzas
vagkaratzas requested changes Feb 11, 2025
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Some comments here and there. Not sure about the container, if it can be in nf-core modules with just that. Is there a similar module?

modules/nf-core/stimulus/checktorchmodel/main.nf Show resolved Hide resolved
modules/nf-core/stimulus/checktorchmodel/main.nf Outdated
container "docker.io/mathysgrapotte/stimulus-py:0.2.4.dev"

input:
path(data)
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no meta? :(

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I've found a way to put it back in, it might be useful

modules/nf-core/stimulus/checktorchmodel/main.nf Outdated Show resolved Hide resolved
modules/nf-core/stimulus/checktorchmodel/main.nf Outdated
# initialize Ray
ray start --head --port=6379 --temp-dir /tmp/ray

# wait or it to start
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Suggested change
# wait or it to start
# wait for it to start

@itrujnara
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I've addressed the comments. I'm still working on the Conda tests.

vagkaratzas
vagkaratzas requested changes Feb 13, 2025
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Almost there. Some more comments, and to find out why the test are failing!

modules/nf-core/stimulus/checktorchmodel/main.nf Outdated
Comment on lines 9 to 10
tuple val(meta), path(data), path(data_config)
tuple val(meta), path(model), path(model_config), path(initial_weights)
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Suggested change
tuple val(meta), path(data), path(data_config)
tuple val(meta), path(model), path(model_config), path(initial_weights)
tuple val(meta) , path(data), path(data_config)
tuple val(meta2), path(model), path(model_config), path(initial_weights)

modules/nf-core/stimulus/checktorchmodel/main.nf Outdated
@@ -0,0 +1,60 @@
process STIMULUS_CHECKTORCHMODEL {
tag "$data_config - $data"
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Why not just:
tag "$meta.id"

modules/nf-core/stimulus/checktorchmodel/main.nf Outdated

script:
def args = task.ext.args ?: ''
prefix = task.ext.prefix ?: model.baseName.replaceFirst(/\.py/, "")
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Just a suggestion here. Instead of trying to parse the model's file name, shouldn't we just use the meta.id as in every other module? You can feed the module the python filename as a meta then, when calling the module.

modules/nf-core/stimulus/checktorchmodel/meta.yml Outdated
pattern: "*.{yml,yaml}"
ontologies:
- edam: "http://edamontology.org/format_3464"
- - meta:
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Suggested change
- - meta:
- - meta2:

@itrujnara
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I've addressed the second review comments. We're aware of failing conda tests and linting and we're working to get the package to conda-forge to fix the problems. If there are any more issues, we'll address them afterwards.

vagkaratzas
vagkaratzas approved these changes Feb 13, 2025
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Good!

vagkaratzas
vagkaratzas requested changes Feb 14, 2025
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I'll be on standby to do a final check after the conda env is fixed.

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@alessiovignoli alessiovignoli alessiovignoli left review comments

@vagkaratzas vagkaratzas vagkaratzas requested changes

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new module: STIMULUS/CHECKTORCHMODEL Turn check_torch_model into an nf-core module
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@itrujnara @vagkaratzas @alessiovignoli