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Add sam2lca/updadb module #7059

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@maxibor maxibor commented Nov 22, 2024

And update sam2lca versions to 1.1.4

PR checklist

  • If you've added a new tool - have you followed the module conventions in the contribution docs
  • 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

@maxibor maxibor requested a review from jfy133 November 25, 2024 10:48
@maxibor maxibor requested a review from a team November 26, 2024 14:44
then {
assertAll(
{ assert process.success }
)
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how is the snapshot created if there is no assertion for it here ?

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I removed the snapshot, and added other assertions

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I think we should at least snapshot the versions and add a snap here :)

modules/nf-core/sam2lca/updatedb/main.nf Outdated Show resolved Hide resolved
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maxibor commented Dec 18, 2024

I believe your suggestions have been adressed @famosab @sateeshperi :)

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I would snapshot at least the versions :)

then {
assertAll(
{ assert process.success }
)
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I think we should at least snapshot the versions and add a snap here :)

"""

stub:
prefix = 'sam2lca_db'
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Suggested change
prefix = 'sam2lca_db'
prefix = task.ext.prefix ?: 'sam2lca_db'

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3 participants