nf-test
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Documentation request: Examples of using profiles in the Configuration documentation
I am attempting to test using different process defaults for some of my modules. It would be convenient if I could specify different profiles to use for testing in different test()
blocks. The configuration documentation makes it seem that this might be possible. However, I cannot figure out how to do this.
For example, I have a default nf_test
profile in my config file. I can specify extra options to be used by the process by using the task.ext
process directive. However, I can't test this in individual test cases because there does not seem to be a straightforward way to select a profile in different tests. e.g. the following immediately fails with "Error: groovy.lang.MissingMethodException: No signature of method: fastp_nf$_run_closure1$_closure4.profile() is applicable for argument types: (String) values: [user_args]"
test("fastp trims reads -- PE reads + user args") {
profile "user_args"
...
}