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Executor google-lifesciences requires workDir, config not recognised #3

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nicolawonggg opened this issue Jan 19, 2023 · 0 comments

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@nicolawonggg
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I am just setting up the first nf-test for our pipeline, so I'm unsure about the compatiblity of things with our pipeline and the test suite.
I am getting an error when running an initial main.nf.test created with the nf-test generate command. The error is seen when running the test on a profile with an executor configuration to run processes the pipeline on Google Life Sciences (GLS).

> nf-test test --profile paths,gcp test/nf-test/main.nf.test

Executor `google-lifesciences` requires a Google Storage bucket to be specified as a working directory -- Add the option `-w gs://<your-bucket/path>` to your run command line or specify a workDir in your config file

Our GLS profile config looks something like this ($params defined in the main nextflow.config):

gcp {
  workDir = "${params.work_path}/${params.full_tag}"

  params.data_path      = "gs://SOME_BUCKET"
  ...
  ...
  process {
    executor      = 'google-lifesciences'
    errorStrategy = { task.exitStatus in [0, 2, 10, 14] && task.attempt < 3 ? 'retry' : 'ignore' }
    maxRetries    = 3
  }
}

I have tried re-defining the workDir in different ways, nf-test doesn't seem to pick them up. I haven't seen any good examples on using the tests/nextflow.config and none of what I've specified there appeared in the meta/params.json. Can someone point me to an example on the use of test-specific config file?

I've also tried running nf-test with another profile for GCP batch, correct me if I'm wrong, but it doesn't seem to be supported in the current version of nf-test.

Appreciate any help, thanks!

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