Add no_filter option working

[FerriolCalvet]

Also update the postprocessing annotation script so that it fails if the output contains duplicated rows.

AI generated summary

This pull request introduces several updates to configuration files and schema definitions, focusing on improving filtering logic, adding new parameters, and removing deprecated configurations. The most significant changes include refactoring the filtering process, introducing new parameters in the schema, and removing unused or redundant configurations.

Filtering logic updates:

• Refactored the filtering logic in conf/modules.config to dynamically construct filters based on the no_filter parameter and the presence of duplex counts (params.all_duplex_counts). This change simplifies and consolidates the filter logic.
• Removed the conf/no_filter.config file, as its functionality is now integrated into the main filtering logic with the no_filter parameter.

Schema updates:

• Added new parameters to nextflow_schema.json, including omega_multi, no_filter, norm_file, and prior_file, to support additional configuration options and enhance flexibility. [1] [2] [3]
• Changed the default value of the confidence_level parameter in nextflow_schema.json from "high" to "med" to align with updated requirements.

Configuration cleanup:

• Removed the no_filter profile from nextflow.config since the no_filter functionality is now handled by the no_filter parameter.
• Deleted commented-out code related to the RUNREGRESSIONS process in conf/modules.config for better code clarity and maintainability.

Additional improvements:

• Updated the PREPARE_INPUT process in conf/tools/hdp_sig_extraction.config to include a publishDir directive for organizing output files.
• Adjusted the file pattern for publishing results in the RUN_HDP_CHAIN_SAMPLING process to restrict it to specific file types (RData, txt, pdf).

[Copilot]

Copilot reviewed 1 out of 8 changed files in this pull request and generated no comments.

Files not reviewed (7)

• conf/bladder.config: Language not supported
• conf/modules.config: Language not supported
• conf/no_filter.config: Language not supported
• conf/tools/hdp_sig_extraction.config: Language not supported
• conf/tools/regressions.config: Language not supported
• nextflow.config: Language not supported
• nextflow_schema.json: Language not supported

[FerriolCalvet]

@FedericaBrando implemented with the no_filter param updating the definition of the ext.filters in the modules.config

[FerriolCalvet]

sorry it is a dirtier PR this time haha 🙏🏻

[FedericaBrando]

The implementation work and it's fine. I have some concerns regarding readability and use of reverse logic in booleans that may lead to confusion.

I've made a small comment in that regard.

Having said that, I think overall it does the job! Good Ferriol! 🚀