Add domain BED automated generation #253
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- not tested - connection with omega missing - decision required on turning on/off of domain annotation generation
missing: - connection to omega
missing: - add params to nextflow_schema - test fail if hotspots on, but nothing else on - test combination of autoexons and BED file together
- add new params to schema - confirm behaviour under different inputs - update script in agreement with behaviour selection - update omega_hotspots param to omega_withingene
FerriolCalvet
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Missing tasks
there are three regions sources:
Each of them can be activated together, or in isolation. If the general omega_withingene is active but none of the others is active or provided, the pipeline will raise an error.
AI generated summary
This pull request introduces several significant changes to configuration files and workflow processes, primarily focusing on the handling of omega hotspots and the introduction of domain annotations. The key changes include renaming parameters, removing redundant BED file configurations, and adding new processes and channels for domain annotations.
Parameter and Configuration Updates:
conf/bladder.config,conf/mice.config,nextflow.config: Renamedomega_hotspotstoomega_withingeneand removedlow_complex_fileandlow_mappability_fileparameters. [1] [2] [3] [4]Workflow and Process Modifications:
modules/local/expand_regions/main.nf: Updated theEXPAND_REGIONSprocess to handle new parameters and logic foromega_autodomainsandomega_autoexons.modules/local/process_annotation/domain/main.nf: Added a new processDOMAIN_ANNOTATIONfor annotating domains.Schema and Subworkflow Changes:
nextflow_schema.json: Renamedhotspot_bedfile_configstoomega_bedfile_configsand added new properties foromega_autodomainsandomega_autoexons. Removedbed_files_options. [1] [2]subworkflows/local/createpanels/main.nf: Included the newDOMAIN_ANNOTATIONprocess and updated the workflow to generate BED files for sequenced domains. [1] [2]Omega Analysis Workflow Updates:
subworkflows/local/omega/main.nf: Modified theOMEGA_ANALYSISworkflow to handle new domain and hotspot file channels.workflows/deepcsa.nf: Updated theDEEPCSAworkflow to use the new domain panel BED file instead of the old hotspots BED file. [1] [2]