nf-test hang on very simple workflow tests

[byb121]

nf-test can hang when running a test on a very simple workflow. Here's the code to replicate the issue:

$ cat example/meaningless_workflow.nf
workflow PipeWf {
    take:
        inputCh

    main:
        inputCh
            | set { outputCh }

    emit:
        outputCh
}

$ cat example/meaningless_workflow.nf.test 

nextflow_workflow {

    name "Test workflow"
    script "example/meaningless_workflow.nf"
    workflow "PipeWf"

    test("PipeWf will hang") {

        when {
            workflow {
                """
                input[0] = Channel.from([
                  [
                    ["patientID": "patientA"],
                    'test_file_1.txt'
                  ]
                ])
                """
            }
        }

        then {
              assert workflow.success
            }

    }

}

$ nf-test test example/meaningless_workflow.nf.test
# This will hang

[lukfor]

Thanks for reporting this.

I see the following in nextflow.log:

Nov-11 15:12:31.429 [main] DEBUG nextflow.Session - Work-dir: /Users/lukfor/Development/git/nf-test/.nf-test/tests/5c41ebd9d6e23bf26ac210b5809436b5/work [Mac OS X]
Nov-11 15:12:31.453 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Nov-11 15:12:31.459 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Nov-11 15:12:31.474 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Nov-11 15:12:31.481 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 9; maxThreads: 1000
Nov-11 15:12:31.521 [main] DEBUG nextflow.Session - Session start invoked
Nov-11 15:12:31.525 [main] DEBUG nextflow.trace.TraceFileObserver - Flow starting -- trace file: /Users/lukfor/Development/git/nf-test/.nf-test/tests/5c41ebd9d6e23bf26ac210b5809436b5/meta/trace.csv
Nov-11 15:12:31.528 [main] DEBUG nextflow.Session - Using default localLib path: /Users/lukfor/Development/git/nf-test/.nf-test/tests/5c41ebd9d6e23bf26ac210b5809436b5/meta/lib
Nov-11 15:12:31.530 [main] DEBUG nextflow.Session - Adding to the classpath library: /Users/lukfor/Development/git/nf-test/.nf-test/tests/5c41ebd9d6e23bf26ac210b5809436b5/meta/lib
Nov-11 15:12:31.907 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Nov-11 15:12:32.023 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: 
Nov-11 15:12:32.025 [main] DEBUG nextflow.Session - Ignite dataflow network (2)
Nov-11 15:12:32.025 [main] DEBUG nextflow.script.ScriptRunner - > Await termination 
Nov-11 15:12:32.025 [main] DEBUG nextflow.Session - Session await
Nov-11 15:12:32.025 [main] DEBUG nextflow.Session - Session await > all process finished
Nov-11 15:12:32.025 [main] DEBUG nextflow.Session - Session await > all barriers passed
Nov-11 15:12:32.032 [main] DEBUG nextflow.Session - This looks weird, attempt number 2 to join pending operators

It seems that Nextflow hang when nf-test tries to serialize the output channels.

[julibeg]

Seconded; new File("${params.nf_test_output}/function.json").text = jsonOutput.toJson(result) in the mock script blocks when only parsing a small CSV.