Add Vizgenpostprocessing/preparesegmentation module

[mcmero]

PR checklist

Closes #8441

• 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

This PR adds the preparesegmentation process for cell segmentation using the vizgen-postprocessing tool for the MERSCOPE spatial omics instrument. The plan would be to add runsegmentationontile​ and compiletilesegmentation​ as subsequent modules to create a segmentation subworkflow for the tool.

The test data is prepared within the test module, using generated dummy data plus an existing segmentation image in nf-core/test-datasets, which needs to be renamed and put in an images directory to work with this module.

I could not find a BioContainer or BioConda package for this tool.

[LouisLeNezet]

Thanks for your contribution.
There is a few modification to make it more nf-core like.

[mcmero]

Thanks you @LouisLeNezet for the review! I've implemented your suggestions. I am getting CI fails now due to an unrelated module. Do you have any suggestions here?

[LouisLeNezet]

Thanks for fixing the modules, this is much better !
Just a few comments before merging.

For the CI fail, something bad migth have happen in another PR.
We will look into it.

[LouisLeNezet]

Suggested change

	tuple val(meta), path("*/*.json"), emit: segmentation_files
	path "versions.yml" , emit: versions
	tuple val(meta), path("${prefix}/*.json"), emit: segmentation_files
	path "versions.yml" , emit: versions

[mcmero]

Using prefix here isn't passing nf-test, I'm not sure why:

╭──────────────────────────────────── nf-test error ────────────────────────────────────╮
│ Assertion failed:                                                                     │
│                                                                                       │
│ assert process.success                                                                │
│        |       |                                                                      │
│        |       false                                                                  │
│        VIZGENPOSTPROCESSING_PREPARESEGMENTATION                                       │
│                                                                                       │
│ java.lang.NullPointerException: Cannot invoke method getAt() on null object           │
│ Assertion failed:                                                                     │
│                                                                                       │
│ assert process.success                                                                │
│        |       |                                                                      │
│        |       false                                                                  │
│        VIZGENPOSTPROCESSING_PREPARESEGMENTATION                                       │
│                                                                                       │
│ java.lang.NullPointerException                                                        │
│                                                                                       │
╰───────────────────────────────────────────────────────────────────────────────────────╯

[LouisLeNezet]

That's strange, it means that the process didn't found the folder "$prefix/".
Is it really created as such ?

[LouisLeNezet]

I tried locally and didn't had any issue...
You need to also remove the def from def prefix = ...

    output:
    tuple val(meta), path("${prefix}/*.json"), emit: segmentation_files
    path "versions.yml"                      , emit: versions

    when:
    task.ext.when == null || task.ext.when

    script:
    ...
    prefix = task.ext.prefix ?: "${meta.id}"
    ...

    stub:
    ...
    prefix = task.ext.prefix ?: "${meta.id}"

[LouisLeNezet]

Suggested change

	- "*/*.json":
	- "${prefix}/*.json":