Add contamination check

[FerriolCalvet]

Add comparison of germline and somatic variants of the cohort to quantify potential intersample contamination

AI summary

This pull request introduces a new process for computing contamination in mutation data and integrates it into the mutation preprocessing workflow. The key changes include adding the COMPUTE_CONTAMINATION process, updating the workflow to use it, and modifying channels to handle the necessary data.

Addition of the COMPUTE_CONTAMINATION process:

• Added a new process COMPUTE_CONTAMINATION in modules/local/contamination/main.nf. This process computes contamination using input mutation files (maf and somatic_maf), outputs contamination results as TSV files, and optionally generates contamination plots as PDFs. It also records the Python version used in a versions.yml file.

Integration into the mutation preprocessing workflow:

• Imported the new COMPUTE_CONTAMINATION process into the mutation preprocessing workflow by adding an include statement in subworkflows/local/mutationpreprocessing/main.nf.
• Updated the MUTATION_PREPROCESSING workflow to create a new channel raw_muts_all_samples by joining metadata with named mutation files, and passed this channel along with muts_all_samples to the COMPUTE_CONTAMINATION process.

[Copilot]

Pull Request Overview

This PR adds a contamination quantification step to the mutation preprocessing workflow by introducing a new COMPUTE_CONTAMINATION process and wiring it into the existing pipeline.

• Added COMPUTE_CONTAMINATION process in modules/local/contamination/main.nf to compute contamination metrics and produce TSV and optional PDF outputs.
• Imported and invoked CONTAMINATION in subworkflows/local/mutationpreprocessing/main.nf, with new channels for raw and somatic mutations.

Reviewed Changes

Copilot reviewed 2 out of 4 changed files in this pull request and generated 2 comments.

File	Description
subworkflows/local/mutationpreprocessing/main.nf	Imported CONTAMINATION and created raw_muts_all_samples channel before invoking contamination step
modules/local/contamination/main.nf	Defined the COMPUTE_CONTAMINATION process with inputs, outputs, script, and stub sections

Comments suppressed due to low confidence (2)

modules/local/contamination/main.nf:10

• The variable name meta2 is ambiguous; consider renaming it to something more descriptive like somatic_meta to clearly distinguish it from the primary meta.

    tuple val(meta2), path(somatic_maf)

modules/local/contamination/main.nf:1

• There are no tests covering the new COMPUTE_CONTAMINATION process. Consider adding unit or integration tests to validate the TSV and PDF outputs under various data scenarios.

process COMPUTE_CONTAMINATION {

[FerriolCalvet]

Good