bug: When an input is passed to output with no modification it causes the snapshot to have the absolute path

[adamrtalbot]

If you pass an input file to an output file directly, the snapshot includes the absolute path of the input file. This causes problems because the snapshot is not transferable.

workflow.nf:

workflow TEST {
    take:
        myFile

    main:
        myFile.view()

    emit:
        myFile
}

workflow.nf.test:

nextflow_workflow {

    name "Test Workflow TEST"
    script "workflow.nf"
    workflow "TEST"

    test("Should run without failures") {

        when {
            workflow {
                """
                // define inputs of the workflow here. Example:
                input[0] = Channel.of(
                    file("test-file.txt")
                )
                """
            }
        }

        then {
            assert workflow.success
            assert snapshot(workflow.out).match()
        }

    }

}

test-file.txt is a blank file.

Resulting snapshot (on my mac):

{
    "Should run without failures": {
        "content": [
            {
                "0": [
                    "/Users/redacted/nf-experiments/.nf-test/tests/d6a81a8faa4b5f7c9b99d042d493a949/test-file.txt"
                ],
                "myFile": [
                    "/Users/redacted/nf-experiments/.nf-test/tests/d6a81a8faa4b5f7c9b99d042d493a949/test-file.txt"
                ]
            }
        ],
        "meta": {
            "nf-test": "0.8.4",
            "nextflow": "23.10.1"
        },
        "timestamp": "2024-03-19T16:00:05.400755"
    }
}

[adamrtalbot]

See https://github.com/nf-core/modules/pull/5278 for an example

[lukfor]

Hi Adam,

thanks, I tried to replicate this issue, but I only see this behaviour if the path of the input file is wrong. I was able to run the test with both empty and non-empty files.

 nextflow_workflow {

    name "Test Workflow TEST"
    script "./workflow.nf"
    workflow "TEST"

    test("Should run without failures") {

        when {
            workflow {
                """
                // define inputs of the workflow here. Example:
                input[0] = Channel.of(
                    file("${moduleDir}/test-file2.txt", checkIfExists: true)
                )
                """
            }
        }

        then {
            assert workflow.success
            assert snapshot(workflow.out).match()
        }

    }

}

See here: https://github.com/askimed/nf-test/commit/d8441aff602247d011fbb377b0cb144f7ecc0574