Don't execute cleanup on dry run

[prototaxites]

Hi, thanks for the fantastic software!

We are running into a small problem with nf-test where we are including the cleanup block in tests. The cleanup block is always executed, which means that exceptions thrown in the block stop the dry run - we are running into this problem with this test (https://github.com/sanger-tol/nf-core-modules/blob/main/modules/sanger-tol/hiccramalign/minimap2align/tests/main.nf.test) where we are using some functions from nft-utils to cleanup a temporary modules library that is initialised in the setup block.

This PR just moves the cleanup line into the section that checks if a dry run is being executed, which should side-step the problem. Not sure if this is the optimal way to do this, so happy to discuss :)

[lukfor]

Thanks! 🙏🏼

[nvnieuwk]

Hi @prototaxites what exceptions are thrown in the setup block?

[prototaxites]

That should say exceptions thrown in the cleanup block... 🤦‍♂️

See https://github.com/sanger-tol/nf-core-modules/blob/main/subworkflows/sanger-tol/cram_map_illumina_hic/tests/main.nf.test for an example - in the setup block we initialise a bunch of files, and then in the cleanup function we run a function that does stuff with those initialised files.

I ended up fixing the function (nfcoreUnlink) but previously it threw an exception if the setup block had not been run first.

[nvnieuwk]

That should say exceptions thrown in the cleanup block... 🤦‍♂️

Yeah that's what I meant 😅, could you provide some small reproducible example? I want to be sure that this is not a deeper problem first

[prototaxites]

main.nf.test:

nextflow_process {

    name "Test Process TEST_MODULE"
    script "./main.nf"
    process "TEST_MODULE"

    tag "test"

    test("test plugin") {

        setup {
            def check_file = new File("${launchDir}/check")
			check_file.text = "hello world"
        }

        then {
            assert process.success
        }
        cleanup {
            def check_file = new File("${launchDir}/check")
            if(!check_file.exists()) {
                throw new Exception("This block should only be seen if setup was not run (i.e. in a dry run)")
            }
        }
    }
}

Testing the following dummy module:

process TEST_MODULE {
    output:
    path ("test.txt"), emit: output

    script:
    """
    echo "hello!" > test.txt
    """
}

Normal run:

> nf-test test main.nf.test

🚀 nf-test 0.9.4
https://www.nf-test.com
(c) 2021 - 2024 Lukas Forer and Sebastian Schoenherr

Warning: This pipeline has no nf-test config file.

Test Process TEST_MODULE

  Test [d53f7783] 'test plugin' PASSED (2.379s)


SUCCESS: Executed 1 tests in 2.381s

Dry run:

> nf-test test main.nf.test --dry-run

🚀 nf-test 0.9.4
https://www.nf-test.com
(c) 2021 - 2024 Lukas Forer and Sebastian Schoenherr

Warning: This pipeline has no nf-test config file.
Dry run mode activated: tests are not executed, just listed.

Test Process TEST_MODULE

  Test [d53f7783] 'test plugin' Error: java.lang.Exception: This block should only be seen if setup was not run (i.e. in a dry run)

[lukfor]

I haven’t checked the code closely for side effects yet, but it makes sense to me that cleanup behaves the same way as setup.