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enryH merged 14 commits into from
Oct 30, 2025
Merged

Update and clarify SDRF and Json-Parameter parsing #596

enryH merged 14 commits into from
Oct 30, 2025

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@enryH enryH commented Oct 24, 2025 •
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PR checklist

  • This comment contains a description of changes (with reason).
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (nextflow run . -profile test_lfq,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test_lfq,docker --outdir <OUTDIR>).
  • Output Documentation in docs/output.md is updated.

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github-actions bot commented Oct 24, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 88d0652

+| ✅ 111 tests passed       |+
#| ❔  19 tests were ignored |#
!| ❗   5 tests had warnings |!
Details

❗ Test warnings:

  • pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
  • pipeline_todos - TODO string in nextflow.config: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
  • pipeline_todos - TODO string in README.md: update the following command to include all required parameters for a minimal example
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.4.1
  • Run at 2025-10-30 06:42:13

@enryH enryH linked an issue Oct 24, 2025 that may be closed by this pull request
Layout how parameters are combined #591
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enryH commented Oct 29, 2025

One suggestion I got is to parse the parameters from the SDRF file using an input schema. assets/input_schema.json, see e.g. sample sheet schema specification. Soon there will be an online tool do it and test the processing.

The samplesheet (SDRF) is parsed part of the UTILS_NEXTFLOW_PIPELINE nf-core template workflow, which then can be the input to BIGBIO_QUANTMS.

To define which parameters are actually used in the end, the ones set in nextflow.config or in the SDRF file is still not entirely clear. I guess it will be rather a documentation issue, although we could think about combining the params map and the sdrf input maps. Dumping can be done using collectfile channel operator.

@enryH enryH marked this pull request as ready for review October 29, 2025 17:01
@enryH enryH requested review from Copilot and ypriverol October 29, 2025 17:01
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enryH commented Oct 29, 2025

@ypriverol It is not really solved. I will need to add a section to the outputs descriptions where I highlight which parameters are picked up from the SDRF file (if provided).

But otherwise the small updates can be merged

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Pull Request Overview

This PR refactors the create_input_channel subworkflow to improve code formatting and modernize Groovy/Nextflow syntax. The changes focus on standardizing code style, replacing a class-based approach with a simpler map structure, and updating function call syntax.

  • Replaced Wrapper class with a map-based structure for storing workflow state
  • Standardized formatting for conditionals, function calls, and assignments
  • Added schema validation for "assay name" field in input JSON

Reviewed Changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated 3 comments.

File Description
subworkflows/local/create_input_channel/main.nf Refactored workflow to use map instead of class, standardized code formatting with consistent spacing and parentheses for function calls
main.nf Added explanatory comment about potential channel usage
assets/schema_input.json Added "assay name" field validation to input schema

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@ypriverol ypriverol requested a review from jpfeuffer October 30, 2025 16:13
@enryH enryH merged commit cad6b0c into dev Oct 30, 2025
36 checks passed
@enryH enryH deleted the params_sdrf_json branch October 30, 2025 16:32
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@ypriverol ypriverol ypriverol approved these changes

@jpfeuffer jpfeuffer Awaiting requested review from jpfeuffer

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Layout how parameters are combined

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