implement sage identification - #13
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julianu
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Mar 16, 2026
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Please fix the small issues.
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Pull request overview
Adds Sage as an additional spectrum identification engine to the nf-core/mspepid pipeline, wiring new parameters through the main workflow and introducing local modules to generate a Sage config and run Sage.
Changes:
- Add
run_sageand Sage-specific parameters (config template + optional prefiltering) across config, schema, and workflows. - Introduce new local modules
SAGECONFIG(config adjustment) andSAGEBETA(Sage search execution) and integrate them intoSPECTRA_IDENTIFICATION. - Add a default Sage JSON config template under
assets/.
Reviewed changes
Copilot reviewed 10 out of 10 changed files in this pull request and generated 13 comments.
Show a summary per file
| File | Description |
|---|---|
| workflows/mspepid.nf | Plumbs Sage parameters through the main MSPEPID workflow into the spectra identification subworkflow. |
| subworkflows/local/spectra_identification/main.nf | Integrates SAGECONFIG + SAGEBETA into the identification stage and mixes Sage outputs into downstream conversion. |
| nextflow_schema.json | Adds schema definitions for Sage parameters and a run_sage toggle. |
| nextflow.config | Adds default Sage params and enables Sage by default. |
| modules/local/sageconfig/meta.yml | New module metadata for Sage config adjustment. |
| modules/local/sageconfig/main.nf | New process to generate an adjusted Sage config JSON based on tolerances/prefilter params. |
| modules/local/sagebeta/meta.yml | New module metadata for Sage execution. |
| modules/local/sagebeta/main.nf | New process to run Sage (beta image) and emit results + version info. |
| main.nf | Sets default Sage config template path and passes Sage args into MSPEPID. |
| assets/default.sage.json | Provides a default Sage configuration template used when none is supplied. |
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Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
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Pull request overview
Adds Sage as an additional search engine to the MSPEPID Nextflow pipeline, wiring new parameters through the main workflow into the spectra identification subworkflow and introducing local modules to generate a Sage config and run Sage.
Changes:
- Add
run_sageand Sage-specific parameters (sage_config_template,sage_prefilter*) to the workflow inputs, defaults, and schema. - Implement Sage execution path in
SPECTRA_IDENTIFICATIONusing newSAGECONFIGandSAGEBETAmodules. - Add a bundled default Sage JSON template and module publish configuration for Sage outputs.
Reviewed changes
Copilot reviewed 11 out of 11 changed files in this pull request and generated 4 comments.
Show a summary per file
| File | Description |
|---|---|
| workflows/mspepid.nf | Plumbs Sage flags/params into the main MSPEPID workflow call to spectra identification. |
| subworkflows/local/spectra_identification/main.nf | Conditionally runs Sage (config generation + search) and mixes results into the identification stream. |
| nextflow_schema.json | Adds schema entries for run_sage and Sage search parameters. |
| nextflow.config | Defines default values for the new Sage parameters. |
| modules/local/sageconfig/meta.yml | Adds nf-core module metadata for Sage config adjustment (has output-key issues). |
| modules/local/sageconfig/main.nf | New process to adjust a Sage config JSON based on tolerances/prefilter params. |
| modules/local/sagebeta/meta.yml | Adds nf-core module metadata for running Sage (has output-key issues + a typo). |
| modules/local/sagebeta/main.nf | New process to run Sage and emit result artifacts + version info. |
| main.nf | Passes new Sage params into the MSPEPID workflow. |
| conf/modules.config | Configures publish behavior for Sage outputs and disables publishing for the intermediate config module. |
| assets/searchengines/default.sage.json | Adds a default Sage configuration template used when no custom template is provided. |
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julianu
approved these changes
Mar 17, 2026
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