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Prototype `nf-test`

Open nvnieuwk opened this issue 2 years ago • 1 comments

Currently contains:

  • A prototype of a simple process (rtgtools/pedfilter) => uses the process testing
  • A prototype of a module that depends on other modules for its input data (multivcfanalyzer) => uses the workflow testing
    • To discuss: Define the input in the workflow itself or in the test file?
  • A prototype of a workflow that needs multiple test cases (aka workflows) (multiqc) => uses the workflow testing
  • A prototype where a specific config file is supplied (mostly helpful to define the args) (gatk4/printsvevidence) => uses workflow testing

IMO the last prototype seems the most suitable to replace all tests with. The developer also noted they will be adding tags and snapshot testing (https://github.com/askimed/nf-test/issues/29). snapshot testing could be a nice replacement for the current yaml implementation

Things that still need to be figured out or worked on:

  • How to set up the tests in GitHub Actions => waiting for the tags feature
  • How to let nf-core/tools generate test files => waiting the yaml or snapshot testing feature

nvnieuwk avatar Oct 10 '22 14:10 nvnieuwk

You need nf-test version 0.6.2 to run the code in this PR

nvnieuwk avatar Oct 11 '22 12:10 nvnieuwk