https://nf-co.re logo
Join Slack
Powered by
Hi, I just updated my tabix modules to HTSLIB_BGZI...
# modules
r
Hi, I just updated my tabix modules to HTSLIB_BGZIPTABIX as recommended because tabix is deprecated but I am getting an error with the singularity container 
htsfile: command not found.
I ran the nf-test for that module using docker and keep getting the error. I am surprised as this appears as a passed test in the modules repo, but might be that it wasn’t tested? Anyone with similar issues? am I missing something obvious? Thanks
m
often there is a upstream problem before that error. can you try to run nf-test with 
--verbose --debug
r
See one of the tests:
Copy code
nf-test test modules/nf-core/htslib/bgziptabix/tests/main.nf.test --verbose --debug

🚀 nf-test 0.9.5
<https://www.nf-test.com>
Please cite: <https://doi.org/10.1093/gigascience/giaf130>
(c) 2021 - 2026 Lukas Forer and Sebastian Schoenherr

Load .nf-test/plugins/nft-bam/0.4.0/nft-bam-0.4.0.jar
Load .nf-test/plugins/nft-utils/0.0.5/nft-utils-0.0.5.jar
Load .nf-test/plugins/nft-vcf/1.0.7/nft-vcf-1.0.7.jar
Warning: Module /Users/manzan01/githubRepos/rnadnavar/subworkflows/nf-core/fastq_align_star/tests/main.nf.test: Dependency '/Users/manzan01/githubRepos/rnadnavar/subworkflows/nf-core/fastq_align_star/tests/../../../../modules/nf-core/rsem/preparereference/main.nf' not found.
Warning: Module /Users/manzan01/githubRepos/rnadnavar/modules/nf-core/picard/filtersamreads/tests/main.nf.test: Dependency '/Users/manzan01/githubRepos/rnadnavar/modules/nf-core/picard/filtersamreads/tests/../../../picard/sortsam/main.nf' not found.

Test Process HTSLIB_BGZIPTABIX

  Test [17de8d4d] 'sarscov2 - vcf - decompress'

    Profiles: [test]
    Configs: [nextflow.config, tests/nextflow.config]
    Command: /Users/manzan01/Software/miniforge3/envs/nf2/bin/nextflow -log /Users/manzan01/githubRepos/rnadnavar/.nf-test/tests/17de8d4dcb05310530c100731b614daa/meta/nextflow.log run /Users/manzan01/githubRepos/rnadnavar/.<http://nf-test-17de8d4dcb05310530c100731b614daa.nf|nf-test-17de8d4dcb05310530c100731b614daa.nf> -c /Users/manzan01/githubRepos/rnadnavar/nextflow.config -c /Users/manzan01/githubRepos/rnadnavar/tests/nextflow.config -params-file /Users/manzan01/githubRepos/rnadnavar/.nf-test/tests/17de8d4dcb05310530c100731b614daa/meta/params.json -ansi-log false -profile test -with-trace /Users/manzan01/githubRepos/rnadnavar/.nf-test/tests/17de8d4dcb05310530c100731b614daa/meta/trace.csv -w /Users/manzan01/githubRepos/rnadnavar/.nf-test/tests/17de8d4dcb05310530c100731b614daa/work
    > Nextflow 26.04.4 is available - Please consider updating your version to it
    > N E X T F L O W  ~  version 26.04.3
    > Launching `/Users/manzan01/githubRepos/rnadnavar/.<http://nf-test-17de8d4dcb05310530c100731b614daa.nf|nf-test-17de8d4dcb05310530c100731b614daa.nf>` [crazy_hopper] - revision: 2f073ddeb8
    > WARN: Task runtime metrics are not reported when using macOS without a container engine
    > [2a/3788f2] Submitted process > HTSLIB_BGZIPTABIX (test)
    > ERROR ~ Error executing process > 'HTSLIB_BGZIPTABIX (test)'
    >
    > Caused by:
    >   Process `HTSLIB_BGZIPTABIX (test)` terminated with an error exit status (127)
    >
    >
    > Command executed:
    >
    >   FILE_TYPE=$(htsfile test.vcf)
    >
    >   case "$FILE_TYPE" in
    >       *BGZF-compressed*)
    >           bgzip -c -d  -@ 2 test.vcf > test.vcf ;;
    >       *gzip-compressed*)
    >           [ "$(basename test.vcf)" == "$(basename test.vcf)" ] && echo "Input and output names cannot be the same" && exit 1
    >           bgzip -d -c -@ 2 test.vcf | cat > test.vcf ;;
    >       *bzip2-compressed*)
    >           bzcat test.vcf | cat > test.vcf ;;
    >       *XZ-compressed*)
    >           xzcat test.vcf | cat > test.vcf ;;
    >       *)
    >            ;;
    >   esac
    >
    > Command exit status:
    >   127
    >
    > Command output:
    >   (empty)
    >
    > Command error:
    >   .command.sh: line 2: htsfile: command not found
    >
    > Work dir:
    >   /Users/manzan01/githubRepos/rnadnavar/.nf-test/tests/17de8d4dcb05310530c100731b614daa/work/2a/3788f2969c346ca1f7bd7f6246e4ab
    >
    > Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
    >
    >  -- Check '/Users/manzan01/githubRepos/rnadnavar/.nf-test/tests/17de8d4dcb05310530c100731b614daa/meta/nextflow.log' file for details
    > Execution cancelled -- Finishing pending tasks before exit

    Stdout:
      N E X T F L O W  ~  version 26.04.3
      Launching `/Users/manzan01/githubRepos/rnadnavar/.<http://nf-test-17de8d4dcb05310530c100731b614daa.nf|nf-test-17de8d4dcb05310530c100731b614daa.nf>` [crazy_hopper] - revision: 2f073ddeb8
      WARN: Task runtime metrics are not reported when using macOS without a container engine
      [2a/3788f2] Submitted process > HTSLIB_BGZIPTABIX (test)
      ERROR ~ Error executing process > 'HTSLIB_BGZIPTABIX (test)'

      Caused by:
        Process `HTSLIB_BGZIPTABIX (test)` terminated with an error exit status (127)


      Command executed:

        FILE_TYPE=$(htsfile test.vcf)

        case "$FILE_TYPE" in
            *BGZF-compressed*)
                bgzip -c -d  -@ 2 test.vcf > test.vcf ;;
            *gzip-compressed*)
                [ "$(basename test.vcf)" == "$(basename test.vcf)" ] && echo "Input and output names cannot be the same" && exit 1
                bgzip -d -c -@ 2 test.vcf | cat > test.vcf ;;
            *bzip2-compressed*)
                bzcat test.vcf | cat > test.vcf ;;
            *XZ-compressed*)
                xzcat test.vcf | cat > test.vcf ;;
            *)
                 ;;
        esac

      Command exit status:
        127

      Command output:
        (empty)

      Command error:
        .command.sh: line 2: htsfile: command not found

      Work dir:
        /Users/manzan01/githubRepos/rnadnavar/.nf-test/tests/17de8d4dcb05310530c100731b614daa/work/2a/3788f2969c346ca1f7bd7f6246e4ab

      Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

       -- Check '/Users/manzan01/githubRepos/rnadnavar/.nf-test/tests/17de8d4dcb05310530c100731b614daa/meta/nextflow.log' file for details
      Execution cancelled -- Finishing pending tasks before exit

    Stderr:
      Nextflow 26.04.4 is available - Please consider updating your version to it

    Nextflow Output:
      N E X T F L O W  ~  version 26.04.3
      Enabled plugins: []
      Disabled plugins: []
      PF4J version 3.14.1 in 'deployment' mode
      No plugins
      Plugin 'nf-schema@2.5.1' resolved
      Start plugin 'nf-schema@2.5.1'
      revision: 2f073ddeb8
      [2a/3788f2] Submitted process > HTSLIB_BGZIPTABIX (test)
      Execution cancelled -- Finishing pending tasks before exit
      Stop plugin 'nf-schema@2.5.1'

        Output Channels:
    {
        "0": [

        ],
        "1": [

        ],
        "2": [

        ],
        "3": [

        ],
        "index": [

        ],
        "output": [

        ],
        "versions_htslib": [

        ],
        "versions_xz": [

        ]
    }
    Topic Channels:
    {

    }
FAILED (13.316s)

  Assertion failed:

  assert process.success
         |       |
         |       false
         HTSLIB_BGZIPTABIX

Assertion failed:

assert process.success
       |       |
       |       false
       HTSLIB_BGZIPTABIX

	at org.codehaus.groovy.runtime.InvokerHelper.createAssertError(InvokerHelper.java:414)
	at main_nf$_run_closure1$_closure2$_closure18.doCall(main.nf.test:31)
	at main_nf$_run_closure1$_closure2$_closure18.doCall(main.nf.test)
	at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103)
	at java.base/java.lang.reflect.Method.invoke(Method.java:580)
	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
	at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
	at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:280)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1009)
	at groovy.lang.Closure.call(Closure.java:433)
	at groovy.lang.Closure.call(Closure.java:412)
	at com.askimed.nf.test.lang.TestCode.execute(TestCode.java:16)
	at com.askimed.nf.test.lang.process.ProcessTest.execute(ProcessTest.java:264)
	at com.askimed.nf.test.core.TestExecutionEngine.execute(TestExecutionEngine.java:172)
	at com.askimed.nf.test.commands.RunTestsCommand.execute(RunTestsCommand.java:322)
	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:39)
	at com.askimed.nf.test.App.main(App.java:46)
  Nextflow stdout:

  N E X T F L O W  ~  version 26.04.3
  Launching `/Users/manzan01/githubRepos/rnadnavar/.<http://nf-test-17de8d4dcb05310530c100731b614daa.nf|nf-test-17de8d4dcb05310530c100731b614daa.nf>` [crazy_hopper] - revision: 2f073ddeb8
  WARN: Task runtime metrics are not reported when using macOS without a container engine
  [2a/3788f2] Submitted process > HTSLIB_BGZIPTABIX (test)
  ERROR ~ Error executing process > 'HTSLIB_BGZIPTABIX (test)'

  Caused by:
    Process `HTSLIB_BGZIPTABIX (test)` terminated with an error exit status (127)


  Command executed:

    FILE_TYPE=$(htsfile test.vcf)

    case "$FILE_TYPE" in
        *BGZF-compressed*)
            bgzip -c -d  -@ 2 test.vcf > test.vcf ;;
        *gzip-compressed*)
            [ "$(basename test.vcf)" == "$(basename test.vcf)" ] && echo "Input and output names cannot be the same" && exit 1
            bgzip -d -c -@ 2 test.vcf | cat > test.vcf ;;
        *bzip2-compressed*)
            bzcat test.vcf | cat > test.vcf ;;
        *XZ-compressed*)
            xzcat test.vcf | cat > test.vcf ;;
        *)
             ;;
    esac

  Command exit status:
    127

  Command output:
    (empty)

  Command error:
    .command.sh: line 2: htsfile: command not found

  Work dir:
    /Users/manzan01/githubRepos/rnadnavar/.nf-test/tests/17de8d4dcb05310530c100731b614daa/work/2a/3788f2969c346ca1f7bd7f6246e4ab

  Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

   -- Check '/Users/manzan01/githubRepos/rnadnavar/.nf-test/tests/17de8d4dcb05310530c100731b614daa/meta/nextflow.log' file for details
  Execution cancelled -- Finishing pending tasks before exit
  Nextflow stderr:
I am also getting failed tests when trying to run it through 
mamba
m
can you try it in a github codespace?
r
On it
same error in codespace
Copy code
/workspaces/rnadnavar -> nf-test test modules/nf-core/htslib/bgziptabix/tests/main.nf.test

🚀 nf-test 0.9.5
<https://www.nf-test.com>
Please cite: <https://doi.org/10.1093/gigascience/giaf130>
(c) 2021 - 2026 Lukas Forer and Sebastian Schoenherr

Load .nf-test/plugins/nft-bam/0.4.0/nft-bam-0.4.0.jar
Load .nf-test/plugins/nft-utils/0.0.5/nft-utils-0.0.5.jar
Load .nf-test/plugins/nft-vcf/1.0.7/nft-vcf-1.0.7.jar
Warning: Module /workspaces/rnadnavar/modules/nf-core/picard/filtersamreads/tests/main.nf.test: Dependency '/workspaces/rnadnavar/modules/nf-core/picard/filtersamreads/tests/../../../picard/sortsam/main.nf' not found.
Warning: Module /workspaces/rnadnavar/subworkflows/nf-core/fastq_align_star/tests/main.nf.test: Dependency '/workspaces/rnadnavar/subworkflows/nf-core/fastq_align_star/tests/../../../../modules/nf-core/rsem/preparereference/main.nf' not found.

Test Process HTSLIB_BGZIPTABIX

  Test [aeb1c9e2] 'sarscov2 - vcf - decompress' FAILED (10.234s)

  Assertion failed:

  assert process.success
         |       |
         |       false
         HTSLIB_BGZIPTABIX

  Nextflow stdout:

  ERROR ~ Error executing process > 'HTSLIB_BGZIPTABIX (test)'

  Caused by:
    Process `HTSLIB_BGZIPTABIX (test)` terminated with an error exit status (127)


  Command executed:

    FILE_TYPE=$(htsfile test.vcf)

    case "$FILE_TYPE" in
        *BGZF-compressed*)
            bgzip -c -d  -@ 2 test.vcf > test.vcf ;;
        *gzip-compressed*)
            [ "$(basename test.vcf)" == "$(basename test.vcf)" ] && echo "Input and output names cannot be the same" && exit 1
            bgzip -d -c -@ 2 test.vcf | cat > test.vcf ;;
        *bzip2-compressed*)
            bzcat test.vcf | cat > test.vcf ;;
        *XZ-compressed*)
            xzcat test.vcf | cat > test.vcf ;;
        *)
             ;;
    esac

  Command exit status:
    127

  Command output:
    (empty)

  Command error:
    .command.sh: line 2: htsfile: command not found

  Work dir:
    /workspaces/rnadnavar/.nf-test/tests/aeb1c9e24000b95b31faca20c9a46b88/work/1c/76bff814fd0b2716bf26f1bb291e68

  Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

   -- Check '/workspaces/rnadnavar/.nf-test/tests/aeb1c9e24000b95b31faca20c9a46b88/meta/nextflow.log' file for details
  Nextflow stderr:



  Test [7058af1e] 'sarscov2 - vcf - compress - index' FAILED (9.364s)

  Assertion failed:

  assert process.success
         |       |
         |       false
         HTSLIB_BGZIPTABIX

  Nextflow stdout:

  ERROR ~ Error executing process > 'HTSLIB_BGZIPTABIX (test)'

  Caused by:
    Process `HTSLIB_BGZIPTABIX (test)` terminated with an error exit status (127)


  Command executed:

    FILE_TYPE=$(htsfile test.vcf)

    case "$FILE_TYPE" in
        *BGZF-compressed*)
            [ '$(basename test.vcf)' != '$(basename test.vcf.gz)' ] && ln -s test.vcf test.vcf.gz ;;
        *gzip-compressed*)
            [ "$(basename test.vcf)" == "$(basename test.vcf.gz)" ] && echo "Input and output names cannot be the same" && exit 1
            bgzip -d -c -@ 2 test.vcf | bgzip -c  -@ 2 > test.vcf.gz ;;
        *bzip2-compressed*)
            bzcat test.vcf | bgzip -c  -@ 2 > test.vcf.gz ;;
        *XZ-compressed*)
            xzcat test.vcf | bgzip -c  -@ 2 > test.vcf.gz ;;
        *)
            bgzip -c  -@ 2 test.vcf > test.vcf.gz ;;
    esac

    tabix -@ 2   -f test.vcf.gz

  Command exit status:
    127

  Command output:
    (empty)

  Command error:
    .command.sh: line 2: htsfile: command not found

  Work dir:
    /workspaces/rnadnavar/.nf-test/tests/7058af1e5e8f8f6d7a2f8c53fcd4b70/work/a7/3e5231e6ff2d3736196b82be4aa9ee

  Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

   -- Check '/workspaces/rnadnavar/.nf-test/tests/7058af1e5e8f8f6d7a2f8c53fcd4b70/meta/nextflow.log' file for details
  Nextflow stderr:
m
can you pull the container directly and look inside with docker?
m
I did implement this new modules in rnavar, and did not notice such issue
you seem to be running with
Copy code
nf-test test modules/nf-core/htslib/bgziptabix/tests/main.nf.test
Do you have 
--profile=+singularity
?
r
Oh, okay. I will take a look at 
rnavar
but I got this error when running the pipeline with singualrity
and whe running with the profile I till get an error:
Copy code
nf-test test modules/nf-core/htslib/bgziptabix/tests/main.nf.test --profile=+docker

🚀 nf-test 0.9.5
<https://www.nf-test.com>
Please cite: <https://doi.org/10.1093/gigascience/giaf130>
(c) 2021 - 2026 Lukas Forer and Sebastian Schoenherr

Load .nf-test/plugins/nft-bam/0.4.0/nft-bam-0.4.0.jar
Load .nf-test/plugins/nft-utils/0.0.5/nft-utils-0.0.5.jar
Load .nf-test/plugins/nft-vcf/1.0.7/nft-vcf-1.0.7.jar
Warning: Module /Users/manzan01/githubRepos/rnadnavar/subworkflows/nf-core/fastq_align_star/tests/main.nf.test: Dependency '/Users/manzan01/githubRepos/rnadnavar/subworkflows/nf-core/fastq_align_star/tests/../../../../modules/nf-core/rsem/preparereference/main.nf' not found.
Warning: Module /Users/manzan01/githubRepos/rnadnavar/modules/nf-core/picard/filtersamreads/tests/main.nf.test: Dependency '/Users/manzan01/githubRepos/rnadnavar/modules/nf-core/picard/filtersamreads/tests/../../../picard/sortsam/main.nf' not found.

Test Process HTSLIB_BGZIPTABIX

  Test [17de8d4d] 'sarscov2 - vcf - decompress' groovy.lang.MissingMethodException: No signature of method: com.askimed.nf.test.lang.process.ProcessContext.sanitizeOutput() is applicable for argument types: (com.askimed.nf.test.lang.channels.Channels) values: [[0:[[[id:test], /Users/manzan01/githubRepos/rnadnavar/.nf-test/tests/17de8d4dcb05310530c100731b614daa/work/b4/247d23a7045fe7002b264f3b54fb20/test.vcf]], ...]]
FAILED (18.62s)

  Assertion failed:

  1 of 3 assertions failed

  Nextflow stdout:

  Nextflow stderr:

  Nextflow 26.04.4 is available - Please consider updating your version to it
m
can you run with --verbose?
s
this error
Copy code
groovy.lang.MissingMethodException: No signature of method: com.askimed.nf.test.lang.process.ProcessContext.sanitizeOutput() is applicable for argument types:
is complaining that your nf-test can't find sanitizeOutput from nf-core-utils, try deleting 
.nf-test
the 
command not found
error usually means that your docker/singularity/conda is not being set properly
r
That is what I thought, but the error appears on my laptop, our hpc and codespace
This si the error in codespace:
Copy code
nf-test test modules/nf-core/htslib/bgziptabix/tests/main.nf.test --profile=+docker --verbose --debug --shard 1/15

🚀 nf-test 0.9.5
<https://www.nf-test.com>
Please cite: <https://doi.org/10.1093/gigascience/giaf130>
(c) 2021 - 2026 Lukas Forer and Sebastian Schoenherr

Load .nf-test/plugins/nft-bam/0.4.0/nft-bam-0.4.0.jar
Load .nf-test/plugins/nft-utils/0.0.5/nft-utils-0.0.5.jar
Load .nf-test/plugins/nft-vcf/1.0.7/nft-vcf-1.0.7.jar
Warning: Module /workspaces/rnadnavar/modules/nf-core/picard/filtersamreads/tests/main.nf.test: Dependency '/workspaces/rnadnavar/modules/nf-core/picard/filtersamreads/tests/../../../picard/sortsam/main.nf' not found.
Warning: Module /workspaces/rnadnavar/subworkflows/nf-core/fastq_align_star/tests/main.nf.test: Dependency '/workspaces/rnadnavar/subworkflows/nf-core/fastq_align_star/tests/../../../../modules/nf-core/rsem/preparereference/main.nf' not found.

Test Process HTSLIB_BGZIPTABIX

  Test [aeb1c9e2] 'sarscov2 - vcf - decompress'

    Profiles: [test, docker]
    Configs: [nextflow.config, tests/nextflow.config]
    Command: /opt/conda/bin/nextflow -log /workspaces/rnadnavar/.nf-test/tests/aeb1c9e24000b95b31faca20c9a46b88/meta/nextflow.log run /workspaces/rnadnavar/.<http://nf-test-aeb1c9e24000b95b31faca20c9a46b88.nf|nf-test-aeb1c9e24000b95b31faca20c9a46b88.nf> -c /workspaces/rnadnavar/nextflow.config -c /workspaces/rnadnavar/tests/nextflow.config -params-file /workspaces/rnadnavar/.nf-test/tests/aeb1c9e24000b95b31faca20c9a46b88/meta/params.json -ansi-log false -profile test,docker -with-trace /workspaces/rnadnavar/.nf-test/tests/aeb1c9e24000b95b31faca20c9a46b88/meta/trace.csv -w /workspaces/rnadnavar/.nf-test/tests/aeb1c9e24000b95b31faca20c9a46b88/work
    > N E X T F L O W  ~  version 26.04.4
    > Launching `/workspaces/rnadnavar/.<http://nf-test-aeb1c9e24000b95b31faca20c9a46b88.nf|nf-test-aeb1c9e24000b95b31faca20c9a46b88.nf>` [sleepy_ampere] - revision: 0a34d241fc
    > [09/5be511] Submitted process > HTSLIB_BGZIPTABIX (test)

    Stdout:
      N E X T F L O W  ~  version 26.04.4
      Launching `/workspaces/rnadnavar/.<http://nf-test-aeb1c9e24000b95b31faca20c9a46b88.nf|nf-test-aeb1c9e24000b95b31faca20c9a46b88.nf>` [sleepy_ampere] - revision: 0a34d241fc
      [09/5be511] Submitted process > HTSLIB_BGZIPTABIX (test)

    Stderr:

    Nextflow Output:
      N E X T F L O W  ~  version 26.04.4
      Enabled plugins: []
      Disabled plugins: []
      PF4J version 3.14.1 in 'deployment' mode
      No plugins
      Plugin 'nf-schema@2.5.1' resolved
      Start plugin 'nf-schema@2.5.1'
      revision: 0a34d241fc
      [09/5be511] Submitted process > HTSLIB_BGZIPTABIX (test)
      Stop plugin 'nf-schema@2.5.1'

        Output Channels:
    {
        "0": [
            [
                {
                    "id": "test"
                },
                "/workspaces/rnadnavar/.nf-test/tests/aeb1c9e24000b95b31faca20c9a46b88/work/09/5be511b3d9babe1073a70a23fae5b9/test.vcf"
            ]
        ],
        "1": [

        ],
        "2": [
            [
                "HTSLIB_BGZIPTABIX",
                "htslib",
                "1.23.1"
            ]
        ],
        "3": [
            [
                "HTSLIB_BGZIPTABIX",
                "xz",
                "5.8.3"
            ]
        ],
        "index": [

        ],
        "output": [
            [
                {
                    "id": "test"
                },
                "/workspaces/rnadnavar/.nf-test/tests/aeb1c9e24000b95b31faca20c9a46b88/work/09/5be511b3d9babe1073a70a23fae5b9/test.vcf"
            ]
        ],
        "versions_htslib": [
            [
                "HTSLIB_BGZIPTABIX",
                "htslib",
                "1.23.1"
            ]
        ],
        "versions_xz": [
            [
                "HTSLIB_BGZIPTABIX",
                "xz",
                "5.8.3"
            ]
        ]
    }
    Topic Channels:
    {

    }
groovy.lang.MissingMethodException: No signature of method: com.askimed.nf.test.lang.process.ProcessContext.sanitizeOutput() is applicable for argument types: (com.askimed.nf.test.lang.channels.Channels) values: [[0:[[[id:test], /workspaces/rnadnavar/.nf-test/tests/aeb1c9e24000b95b31faca20c9a46b88/work/09/5be511b3d9babe1073a70a23fae5b9/test.vcf]], ...]]
FAILED (20.389s)

  Assertion failed:

  1 of 3 assertions failed

Assertion failed:

1 of 3 assertions failed

        at com.askimed.nf.test.lang.extensions.GlobalMethods.assertAll(GlobalMethods.java:47)
        at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
        at main_nf$_run_closure1$_closure2$_closure18.doCall(main.nf.test:32)
        at main_nf$_run_closure1$_closure2$_closure18.doCall(main.nf.test)
        at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103)
        at java.base/java.lang.reflect.Method.invoke(Method.java:580)
        at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
        at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
        at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:280)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1009)
        at groovy.lang.Closure.call(Closure.java:433)
        at groovy.lang.Closure.call(Closure.java:412)
        at com.askimed.nf.test.lang.TestCode.execute(TestCode.java:16)
        at com.askimed.nf.test.lang.process.ProcessTest.execute(ProcessTest.java:264)
        at com.askimed.nf.test.core.TestExecutionEngine.execute(TestExecutionEngine.java:172)
        at com.askimed.nf.test.commands.RunTestsCommand.execute(RunTestsCommand.java:322)
        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:39)
        at com.askimed.nf.test.App.main(App.java:46)
  Nextflow stdout:

  N E X T F L O W  ~  version 26.04.4
  Launching `/workspaces/rnadnavar/.<http://nf-test-aeb1c9e24000b95b31faca20c9a46b88.nf|nf-test-aeb1c9e24000b95b31faca20c9a46b88.nf>` [sleepy_ampere] - revision: 0a34d241fc
  [09/5be511] Submitted process > HTSLIB_BGZIPTABIX (test)
  Nextflow stderr:





FAILURE: Executed 1 tests in 20.452s (1 failed)
m
What's your version on nft-utils in the nf-test.config file?
r
nft-utils@0.0.5
Mmm quite old isn’t it?
m
Try 1.0.0
r
Right… now it works 😄
Thank you Maxime, it was driving me crazy!!
I wasn’t even aware of this plugin
m
Sorry for not catching the issue earlier
Let's plan a catch-up meeting soon and maybe do a session to push forward
r
No worries at all, thank you everyone for helping with the debugging
Yes, happy to do so
s
Do we need to check for that via nf-core modules install?
m
These are module tests, I actually don't usually recommend to run them, since they're already tested upstream
s
Sure, and they are ignored by default in the pipeline template
5 Views
Open in Slack
PreviousNext
Powered by