Separation of artifactual filter from somatic filter

[FerriolCalvet]

Human summary

• reordered blacklisting of mutations
• add clean mutations module
• tested

FIRST FILTER (for generating CLEANMUTATIONS)

{
    "DEPTH" : "ge 40",  "FILTER" : ["notcontains NM20", "notcontains p8", "notcontains n_rich", "notcontains cohort_n_rich_threshold", "notcontains cohort_n_rich", "notcontains no_pileup_support", "notcontains low_mappability", "notcontains not_covered"], "VAF_distorted_expanded_sq" : false
}

SECOND FILTER (for generating SOMATICMUTATIONS)

{
    "VAF" : "le 0.3",   "VAF_AM" : "le 0.3",    "vd_VAF" : "le 0.3",    "FILTER" : []
}

new diagram of this subworkflow

AI summary

This pull request introduces several significant updates to the mutation preprocessing workflow, focusing on the addition of new filtering steps and the refinement of existing processes. The main changes include adding new modules for cleaning and filtering mutations, updating configuration parameters, and modifying the workflow to incorporate these new steps.

Key Changes:

Workflow Enhancements:

• Added new mutation cleaning and filtering steps (CLEANMUTATIONS and SOMATICMUTATIONS) to the workflow to refine mutation data before final processing. (subworkflows/local/mutationpreprocessing/main.nf) [1] [2]

Configuration Updates:

• Introduced a new configuration parameter filter_criteria_somatic to specify filters for somatic mutations, and updated the description for filter_criteria. (nextflow.config)
• Updated the schema to include filter_criteria_somatic and revised the description for filter_criteria. (nextflow_schema.json)

Module Additions:

• Added new modules WRITEMAF, CLEANMUTATIONS, and SOMATICMUTATIONS to the process configuration to handle different stages of mutation filtering and output. (conf/modules.config)
• Included the CLEANMUTATIONS module in the mutation preprocessing workflow to clean artifact mutations. (subworkflows/local/mutationpreprocessing/main.nf)

These changes collectively enhance the mutation preprocessing workflow by adding more granular control over mutation filtering and ensuring cleaner data for downstream analysis.

[Copilot]

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Files not reviewed (4)

• conf/modules.config: Language not supported
• nextflow.config: Language not supported
• nextflow_schema.json: Language not supported
• subworkflows/local/mutationpreprocessing/main.nf: Language not supported

[FerriolCalvet]

looks good and tested