fix: CLIN-2414 allow to pass exomiser spring options in task.ext

[LysianeBouchard]

It appears that exomiser options overriding properties in application.properties must be passed at the end of the exomiser command. Any command-line options specified after these overrides seem to be ignored, causing various buggy behaviors.

We have observed a specific instance of this problem before but were not aware of the precise cause. To avoid this issue, we initially decided to pass task.ext.args at the beginning of the command. However, this fix has caused other problems in different contexts, particularly in QLIN, where passing an application property is required.

This PR allows passing both regular CLI options and options for application properties. We will use two different task.ext keys.

Manual Tests

• Run the pipeline in the Qlin environment, using exomiser 13.1.0, with realistic configuration files, as will be done when integrating the pipeline in the qlin etl. The exomiser process now runs correctly and we can see the exomiser files correctly in the output folder. ✅

• Run the pipeline locally, i.e. with nextflow run main.nf -profile test,docker. The pipeline runs successfully. We see the exomiser output files in the output folder. ✅

• Repeat the same test in Juno ✅

• By default, we don't override exomiser application properties when using the test profile. We passed an extra configuration file with the following content:

process {
 withName: EXOMISER { 
        ext.application_properties_args = { "--logging.file.name=results/logs.exomiser.json" }
 }
}

The pipeline should run successfully and we should see the file logs.exomiser.json in exomiser output folder. ✅

• Repeat the same test in Juno ✅

PR checklist

• 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 pipeline conventions in the contribution docs
• Make sure your code lints (nf-core lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• Reference Data Documentation in docs/reference_data.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[georgette-femerling]

Looks good!