Adding met-excision as parameter to DIA and DDA workflows

[ypriverol]

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[Copilot]

Pull Request Overview

This pull request adds a new boolean parameter ("met_excision") to support methionine excision in the DIA and DDA workflows.

• Introduces the new met_excision parameter in the JSON schema with descriptive help text.
• Sets met_excision to true by default in nextflow.config.
• Updates the DIANN in silico library generation process to optionally include the --met-excision flag.
• Updates CHANGELOG.md to document the changes.

Reviewed Changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated 1 comment.

File	Description
nextflow_schema.json	Adds the new met_excision parameter to the workflow schema
nextflow.config	Enables the met_excision parameter by default
modules/local/diann/insilico_library_generation/main.nf	Updates DIANN command to conditionally include the --met-excision flag
CHANGELOG.md	Documents updates including the met_excision change

[Copilot]

Pull Request Overview

This PR adds support for methionine excision as a configurable parameter in both DIA and DDA workflows.

• Introduces a new boolean parameter "met_excision" in nextflow_schema.json with default true and associated documentation.
• Updates nextflow.config to enable methionine excision by default.
• Modifies COMET and DIANN modules to include the respective command-line flags for methionine excision, and updates CHANGELOG.md accordingly.

Reviewed Changes

Copilot reviewed 5 out of 5 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
nextflow_schema.json	Adds the "met_excision" parameter with detailed help text
nextflow.config	Sets the default for met_excision
modules/local/openms/comet/main.nf	Passes the met_excision flag for COMET workflows
modules/local/diann/insilico_library_generation/main.nf	Passes the met_excision flag for DIANN workflows
CHANGELOG.md	Documents the addition of methionine excision support

[Copilot]

Pull Request Overview

This PR adds support for an optional met-excision parameter to both the DIA and DDA workflows. Key changes include updating the Nextflow schema and configuration to include the new boolean parameter, and propagating the parameter into both the COMET and DIANN modules with appropriate command line flags.

Reviewed Changes

Copilot reviewed 5 out of 5 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
nextflow_schema.json	Added met_excision parameter definition with schema details
nextflow.config	Set met_excision default value in workflow parameters
modules/local/openms/comet/main.nf	Integrated met_excision flag into the COMET command line options
modules/local/diann/insilico_library_generation/main.nf	Integrated met_excision flag into the DIANN library generation command
CHANGELOG.md	Updated changelog documenting the new met-excision feature

Comments suppressed due to low confidence (2)

modules/local/openms/comet/main.nf:82

• Verify that the COMET command line flag '-clip_nterm_methionine true' is fully supported and correctly interpreted by the tool, especially given potential updates to its interface.

met_excision = params.met_excision ? "-clip_nterm_methionine true" : ""

modules/local/diann/insilico_library_generation/main.nf:29

• Ensure that the '--met-excision' flag passed to DIANN is handled as intended, and consider documenting any expected behavior or constraints for this flag.

met_excision = params.met_excision ? "--met-excision" : ""