Add nf-test to porechop_abi

[LilyAnderssonLee]

PR checklist

Will be used in nf-core/taxprofiler#145

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the module conventions in the contribution docs
• If necessary, include test data in your PR.
• Remove all TODO statements.
• Emit the versions.yml file.
• Follow the naming conventions.
• Follow the parameters requirements.
• Follow the input/output options guidelines.
• Add a resource label
• Use BioConda and BioContainers if possible to fulfil software requirements.
• Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
  • For modules:
    • nf-core modules test <MODULE> --profile docker
    • nf-core modules test <MODULE> --profile singularity
    • nf-core modules test <MODULE> --profile conda
  • For subworkflows:
    • nf-core subworkflows test <SUBWORKFLOW> --profile docker
    • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
    • nf-core subworkflows test <SUBWORKFLOW> --profile conda

[SPPearce]

Can you also please add the check that the input/output files do not match.

[SPPearce]

Don't forget to the remove the pytest files too (including from the config).

[LilyAnderssonLee]

Don't forget to the remove the pytest files too (including from the config).

Do I need to include config to the test? Do you have an example of this?

[SPPearce]

Don't forget to the remove the pytest files too (including from the config).

Do I need to include config to the test? Do you have an example of this?

Sorry, I mean you need to remove them from:
https://github.com/nf-core/modules/blob/master/tests/config/pytest_modules.yml
to stop the pytest tests from being ran.

[LilyAnderssonLee]

The process tests passed, but the stability check still fails. It seems that redirecting the log file is not correct, right?

│   Test [256ae19c] 'sarscov2-nanopore' FAILED (9.769s)                                                                         │
│                                                                                                                               │
│   Assertion failed:                                                                                                           │
│                                                                                                                               │
│   1 of 2 assertions failed                                                                                                    │
│                                                                                                                               │
│   Nextflow stdout:                                                                                                            │
│                                                                                                                               │
│   Nextflow stderr:     

[SPPearce]

The process tests passed, but the stability check still fails. It seems that redirecting the log file is not correct, right?

│   Test [256ae19c] 'sarscov2-nanopore' FAILED (9.769s)                                                                         │
│                                                                                                                               │
│   Assertion failed:                                                                                                           │
│                                                                                                                               │
│   1 of 2 assertions failed                                                                                                    │
│                                                                                                                               │
│   Nextflow stdout:                                                                                                            │
│                                                                                                                               │
│   Nextflow stderr:     

It may well mean that the log file contains a timestamp, and hence changes every time.
Let me take a look

[SPPearce]

No timestamp, but the last line of the log includes the full path:
Saved result to /workspace/modules/.nf-test/tests/7da04198d79b5b8b0117b170c3e2ef14/work/62/b69f2df1551d4b60ecf77f32ab8ab0/test.porechop_abi.fastq.gz
So we need to exclude this from the snapshot.
I can't push to your branch because it is on your own repo.

[LilyAnderssonLee]

@SPPearce Is it ready to me merged?

[SPPearce]

Yep, looks good to me now.