Set minimum mutations per sample threshold

[FerriolCalvet]

Samples with no mutations are not analyzed individually

• same happens with groups that have less than a the chosen number of muts
• set minimum to 0

[Copilot]

Pull Request Overview

This PR introduces a configurable minimum mutations per sample threshold to control when individual sample analysis is performed. It sets a new parameter with a default value of 0 to ensure samples with no mutations are not excluded from analysis.

• Added configurable min_muts_per_sample parameter with default value of 0
• Modified mutation subset process to handle optional output when minimum threshold is not met
• Removed "notcontains p8" from default filter criteria

Reviewed Changes

Copilot reviewed 4 out of 5 changed files in this pull request and generated 2 comments.

File	Description
nextflow_schema.json	Added schema definition for the new min_muts_per_sample parameter
nextflow.config	Added min_muts_per_samples parameter and updated filter criteria
modules/local/subsetmaf/main.nf	Modified process to accept minimum mutations parameter and made output optional
conf/modules.config	Applied minimum mutations parameter to SOMATICMUTATIONS process

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