Stranger

[gustav-001]

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 pipelines 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.
• Parameters Documentation is updated with nf-core schema docs --format markdown --output docs/parameters.md --force
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

Description

Adds Stranger to the repeat-expansion subworkflow, annotating ExpansionHunter's calls with pathogenicity classification taken from the variant catalog.

Changes

• EXPANSIONHUNTER → BCFTOOLS_ANNOTATE → TABIX_TABIX becomes EXPANSIONHUNTER → BCFTOOLS_ANNOTATE → STRANGER
• TABIX_TABIX is removed as Stranger emits its own .tbi.
• The catalog channel take is reused.
• ext.prefix is necessary, otherwise the module errors due to matching in- and output filenames.

Issues

• This was tested with a local copy of a modified variant_catalog.json file with the necessary fields for Stranger. This file is not live on the test-datasets repo. The new variant_catalog_stranger.json can be used as input for ExpansionHunter as additional fields are ignored.

[nvnieuwk]

Allright! Still some broken tests that need to be fixed though

[gustav-001]

Allright! Still some broken tests that need to be fixed though

Some tests are failing due to the variant catalog file not having the required fields for Stranger. I opened a PR for this on the tests-datasets repo. Can you check that one out? Thanks

[nvnieuwk]

Approved and merged!

[nvnieuwk]

Looks good! Thank you