Dummy PR: Debugging nf-test ngscheckmate/ncm in Sarek

[asp8200]

Dummy PR - don't merge!

I can't run the following nf-test in Sarek:

nf-test test --profile=docker --verbose --debug modules/nf-core/ngscheckmate/ncm --updateSnapshot

There are a couple of issues with the nf-test for ngscheckmate/ncm, in particular, it assumes that the module bedtools/makewindows is installed.

With the changes in this dummy PR, I got 3 out of 4 tests working.

What follows it the log from the failing test:

  Test [214966b7] 'sarscov2 - vcf'

    Profiles: [docker]
    Configs: [nextflow.config, conf/test.config, /home/ubuntu/dev/sarek_maxulysse/modules/nf-core/ngscheckmate/ncm/tests/./nextflow.config, /home/ubuntu/dev/sarek_maxulysse/modules/nf-core/ngscheckmate/ncm/tests/./vcf.config]
    Command: /home/ubuntu/mambaforge/envs/nf-core/bin/nextflow -log /home/ubuntu/dev/sarek_maxulysse/.nf-test/tests/214966b78ba50a966671851e09d892cd/meta/nextflow.log run /home/ubuntu/dev/sarek_maxulysse/.nf-test/tests/214966b78ba50a966671851e09d892cd/meta/mock.nf -c /home/ubuntu/dev/sarek_maxulysse/nextflow.config -c /home/ubuntu/dev/sarek_maxulysse/conf/test.config -c /home/ubuntu/dev/sarek_maxulysse/modules/nf-core/ngscheckmate/ncm/tests/./nextflow.config -c /home/ubuntu/dev/sarek_maxulysse/modules/nf-core/ngscheckmate/ncm/tests/./vcf.config -params-file /home/ubuntu/dev/sarek_maxulysse/.nf-test/tests/214966b78ba50a966671851e09d892cd/meta/params.json -ansi-log false -profile docker -with-trace /home/ubuntu/dev/sarek_maxulysse/.nf-test/tests/214966b78ba50a966671851e09d892cd/meta/trace.csv -w /home/ubuntu/dev/sarek_maxulysse/.nf-test/tests/214966b78ba50a966671851e09d892cd/work
    > N E X T F L O W  ~  version 24.04.2
    > Launching `/home/ubuntu/dev/sarek_maxulysse/.nf-test/tests/214966b78ba50a966671851e09d892cd/meta/mock.nf` [dreamy_minsky] DSL2 - revision: fc1da8e981
    > [35/3ce065] Submitted process > BEDTOOLS_MAKEWINDOWS (test)

    Stdout:
      N E X T F L O W  ~  version 24.04.2
      Launching `/home/ubuntu/dev/sarek_maxulysse/.nf-test/tests/214966b78ba50a966671851e09d892cd/meta/mock.nf` [dreamy_minsky] DSL2 - revision: fc1da8e981
      [35/3ce065] Submitted process > BEDTOOLS_MAKEWINDOWS (test)

    Stderr:

    Nextflow Output:
      N E X T F L O W  ~  version 24.04.2
      Enabled plugins: []
      Disabled plugins: []
      PF4J version 3.10.0 in 'deployment' mode
      No plugins
      revision: fc1da8e981
      Plugin 'nf-validation@1.1.3' resolved
      Start plugin 'nf-validation@1.1.3'
      Plugin 'nf-prov@1.2.2' resolved
      Start plugin 'nf-prov@1.2.2'
      Plugin 'nf-amazon@2.5.2' resolved
      Start plugin 'nf-amazon@2.5.2'
      [35/3ce065] Submitted process > BEDTOOLS_MAKEWINDOWS (test)
      Stop plugin 'nf-amazon@2.5.2'
      Stop plugin 'nf-prov@1.2.2'
      Stop plugin 'nf-validation@1.1.3'

        Output Channels:
    {
        "0": [

        ],
        "1": [

        ],
        "2": [

        ],
        "3": [

        ],
        "4": [

        ],
        "5": [

        ],
        "all": [

        ],
        "corr_matrix": [

        ],
        "matched": [

        ],
        "pdf": [

        ],
        "vcf": [

        ],
        "versions": [

        ]
    }
java.lang.NullPointerException: Cannot invoke method getAt() on null object
FAILED (11.025s)

  Assertion failed:

  1 of 2 assertions failed

Assertion failed:

1 of 2 assertions failed

	at com.askimed.nf.test.lang.extensions.GlobalMethods.assertAll(GlobalMethods.java:48)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:568)
	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
	at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
	at org.codehaus.groovy.runtime.callsite.StaticMetaMethodSite.invoke(StaticMetaMethodSite.java:44)
	at org.codehaus.groovy.runtime.callsite.StaticMetaMethodSite.callStatic(StaticMetaMethodSite.java:100)
	at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallStatic(CallSiteArray.java:55)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callStatic(AbstractCallSite.java:217)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callStatic(AbstractCallSite.java:240)
	at main_nf$_run_closure1$_closure4$_closure20.doCall(main.nf.test:120)
	at main_nf$_run_closure1$_closure4$_closure20.doCall(main.nf.test)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:568)
	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
	at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
	at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:274)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1030)
	at groovy.lang.Closure.call(Closure.java:427)
	at groovy.lang.Closure.call(Closure.java:406)
	at com.askimed.nf.test.lang.TestCode.execute(TestCode.java:16)
	at com.askimed.nf.test.lang.process.ProcessTest.execute(ProcessTest.java:169)
	at com.askimed.nf.test.core.TestExecutionEngine.execute(TestExecutionEngine.java:214)
	at com.askimed.nf.test.commands.RunTestsCommand.execute(RunTestsCommand.java:184)
	at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:43)
	at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:18)
	at picocli.CommandLine.executeUserObject(CommandLine.java:1953)
	at picocli.CommandLine.access$1300(CommandLine.java:145)
	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2352)
	at picocli.CommandLine$RunLast.handle(CommandLine.java:2346)
	at picocli.CommandLine$RunLast.handle(CommandLine.java:2311)
	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179)
	at picocli.CommandLine.execute(CommandLine.java:2078)
	at com.askimed.nf.test.App.run(App.java:44)
	at com.askimed.nf.test.App.main(App.java:51)
  Nextflow stdout:

  N E X T F L O W  ~  version 24.04.2
  Launching `/home/ubuntu/dev/sarek_maxulysse/.nf-test/tests/214966b78ba50a966671851e09d892cd/meta/mock.nf` [dreamy_minsky] DSL2 - revision: fc1da8e981
  [35/3ce065] Submitted process > BEDTOOLS_MAKEWINDOWS (test)
  Nextflow stderr: