feat: CLIN-3686 add support for local source in exomiser

[LysianeBouchard]

Add support for the LOCAL frequency source in exomiser.

To use this feature, you must provide the following parameters with full paths:

• exomiser_local_frequency_path
• exomiser_local_frequency_index_path

The index file is required if using the feature, meaning exomiser_local_frequency_index_path must be specified if exomiser_local_frequency_path is provided.

Additionally, add the LOCAL keyword to the frequency sources definition in the exomiser analysis file.

Our test setup covers the local source, so you can use it as an example.

Other change:

• Add extra java -Xmx option (maximum heap size) in exomiser command as in standard nf-core processes

Tests

-Run the test profile locally:
nextflow run main.nf -profile test,docker
We should see a log message from exomiser indicating that a local frequency file is used

-Comment the line defining the exomiser_local_frequency_index_path in test configuration.
Then run the pipeline again. It should fail with a warning mentioning that the parameter exomiser_local_frequency_index_path is missing.

-Comment the LOCAL source in assets/exomiser/test_exomiser_analysis
Comment the lines defining the exomiser_local_frequency_path and exomiser_local_frequency_index_path parameters in test profile
Then run:
nextflow run main.nf -profile test,docker
The pipeline should run successfully.
We should not see the log message for the local frequency file

• Replicate tests 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).

[FelixAntoineLeSieur]

Not 100% familiar with the exomiser options, but seems good to me!