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Add configuration option for Nextflow work directory management - #368

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Add configuration option for Nextflow work directory management#368
k-florek wants to merge 1 commit into
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This pull request introduces a new configuration option, useWorkDir, to allow users to delegate work directory management to Nextflow instead of nf-test. This is particularly useful for running tests in cloud environments the work directory is on a separate host from where nf-test is running. The implementation ensures that the work directory specified by nf-test is only created and passed to Nextflow if useWorkDir is enabled.

This would address issue #78 and #91

Configuration enhancements:

  • Added the useWorkDir option to the nf-test.config configuration file, allowing users to control whether nf-test or Nextflow manages the work directory. The default is true.
  • Updated the Config class to include the useWorkDir property, along with its getter and setter methods. [1] [2]

Conditional work directory handling:

  • Modified AbstractTest to only create and set up the work directory if useWorkDir is enabled. [1] [2]
  • Updated PipelineTest, ProcessTest, and WorkflowTest to only pass the work directory to Nextflow if useWorkDir is enabled. [1] [2] [3]
  • Improved TestContext initialization to handle cases where the work directory may not be set (i.e., when useWorkDir is false).

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