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Merged
merged 2 commits into from
Jul 17, 2025
Merged

README_links #560

merged 2 commits into from
Jul 17, 2025

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enryH
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@enryH enryH commented Jun 5, 2025 •
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User description

  • README.md is updated (including new tool citations and authors/contributors).

PR Type

Documentation

Description

• Added optional ms2rescore step to both DDA-LFQ and DDA-ISO workflows
• Fixed broken GitHub link from bigbio to bibgio repository
• Updated ProteomicsLFQ documentation links from UTILS to TOPP
• Renumbered workflow steps to accommodate new optional step

Changes walkthrough 📝

Relevant files
Documentation
README.md
Update workflow documentation and fix links                           

README.md

• Added optional ms2rescore step to DDA-LFQ and DDA-ISO workflows
•
Fixed GitHub repository link from bigbio to bibgio
• Updated
ProteomicsLFQ documentation URLs from UTILS to TOPP
• Renumbered
workflow steps to accommodate new optional step

 +17/-15 
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    qodo-merge-pro bot commented Jun 5, 2025 •
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    CI Feedback 🧐

    (Feedback updated until commit ccb7db2)

    A test triggered by this PR failed. Here is an AI-generated analysis of the failure:

    Action: template_version

    Failed stage: Post nf-core template version comment [❌]

    Failure summary:

    The action failed because the required input parameter repo-token was not supplied. This is a GitHub
    Actions configuration error where the workflow is missing the necessary authentication token to
    perform repository operations.

    Relevant error logs: 
    1:  ##[group]Operating System
2:  Ubuntu
...

449:  > Newer version of the nf-core template is available.
450:  >
451:  > Your pipeline is using an old version of the nf-core template: 3.2.1.
452:  > Please update your pipeline to the latest version.
453:  >
454:  > For more documentation on how to update your pipeline, please see the [nf-core documentation](https://github.com/nf-core/tools?tab=readme-ov-file#sync-a-pipeline-with-the-template) and [Synchronisation documentation](https://nf-co.re/docs/contributing/sync).
455:  
456:  message-id: add-pr-comment
457:  refresh-message-position: false
458:  repo-owner: bigbio
459:  repo-name: quantms
460:  status: success
461:  env:
462:  OUTPUT: nf-core          3.2.1          3.3.1       wheel
463:  ##[endgroup]
464:  ##[error]Input required and not supplied: repo-token
465:  Post job cleanup.

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    github-actions bot commented Jun 5, 2025 •
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    nf-core pipelines lint overall result: Passed ✅ ⚠️

    Posted for pipeline commit ccb7db2

    +| ✅  99 tests passed       |+
#| ❔  17 tests were ignored |#
!| ❗  14 tests had warnings |!

    ❗ Test warnings:

    • pipeline_todos - TODO string in ro-crate-metadata.json: "description": "

      \n \n <source media="(prefers-color-scheme: dark)" srcset="docs/images/bigbio-quantms_logo_dark.png">\n <img alt="bigbio/quantms" src="docs/images/bigbio-quantms_logo_light.png">\n \n

      \n\nGitHub Actions CI Status\nGitHub Actions Linting StatusAWS CICite with Zenodo\nnf-test\n\nNextflow\nrun with conda\nrun with docker\nrun with singularity\nLaunch on Seqera Platform\n\nGet help on SlackFollow on TwitterFollow on MastodonWatch on YouTube\n\n## Introduction\n\nbigbio/quantms is a bioinformatics pipeline that ...\n\n TODO nf-core:\n Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n major pipeline sections and the types of output it produces. You're giving an overview to someone new\n to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n\n\n Include a figure that guides the user through the major workflow steps. Many nf-core\n workflows use the "tube map" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples. \n Fill in short bullet-pointed list of the default steps in the pipeline 1. Read QC (FastQC)2. Present QC for raw reads (MultiQC)\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.\n\n Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\nsamplesheet.csv:\n\ncsv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n\n\nNow, you can run the pipeline using:\n\n update the following command to include all required parameters for a minimal example \n\nbash\nnextflow run bigbio/quantms \\\n -profile <docker/singularity/.../institute> \\\n --input samplesheet.csv \\\n --outdir <OUTDIR>\n\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.\n\nFor more details and further functionality, please refer to the usage documentation and the parameter documentation.\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the results tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\noutput documentation.\n\n## Credits\n\nbigbio/quantms was originally written by Yasset Perez-Riverol.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n If applicable, make list of people who have also contributed \n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the contributing guidelines.\n\nFor further information or help, don't hesitate to get in touch on the Slack #quantms channel (you can join with this invite).\n\n## Citations\n\n Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. \n If you use bigbio/quantms for your analysis, please cite it using the following doi: 10.5281/zenodo.XXXXXX \n\n Add bibliography of tools and data used in your pipeline \n\nAn extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.\n\nYou can cite the nf-core publication as follows:\n\n> The nf-core framework for community-curated bioinformatics pipelines.\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.\n",
    • 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 README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
    • pipeline_todos - TODO string in README.md: Add bibliography of tools and data used in your pipeline
    • 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 main.nf: Optionally add in-text citation tools to this list.
    • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
    • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
    • 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 base.config: Check the defaults for all processes
    • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
    • local_component_structure - samplesheet_check.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
    • local_component_structure - preprocess_expdesign.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure

    ❔ Tests ignored:

    ✅ Tests passed:

    Run details

    • nf-core/tools version 3.2.1
    • Run at 2025-06-12 14:39:17

    @enryH enryH marked this pull request as ready for review June 11, 2025 16:11
    @qodo-merge-pro Qodo Merge Pro
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    PR Reviewer Guide 🔍

    Here are some key observations to aid the review process:

    ⏱️ Estimated effort to review: 1 🔵⚪⚪⚪⚪
    🧪 No relevant tests
    🔒 No security concerns identified
    ⚡ Recommended focus areas for review

    Broken Link

    The GitHub repository link still points to bigbio instead of bibgio in the openms fdr tool reference, which appears to be inconsistent with the PR description claiming this was fixed.

     
    5. Peptide identification FDR [`openms fdr tool`](https://github.com/bibgio/quantms/blob/dev/modules/local/openms/falsediscoveryrate/main.nf)
6. Modification localization [`luciphor`](https://github.com/dfermin/lucXor)
    Link Inconsistency

    The Epifany tool link in the DDA-ISO workflow still uses UTILS instead of TOPP, which is inconsistent with other documentation link updates in this PR.

     
    8. Protein inference [`ProteinInference`](https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_ProteinInference.html) or [`Epifany`](https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_Epifany.html) for bayesian inference.
9. Protein Quantification [`ProteinQuantifier`](https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_ProteinQuantifier.html)

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    qodo-merge-pro bot commented Jun 11, 2025 •
    edited
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    PR Code Suggestions ✨

    Explore these optional code suggestions:

    CategorySuggestion                                                                                                                                    Impact
    Possible issue
    ✅ Fix repository URL typo
    Suggestion Impact:The suggestion identified a typo in the GitHub URL that was fixed in the commit. The commit corrected "bibgio" to "bigbio" in multiple locations, though it also made additional changes to the URLs (changing branch from "dev" to "HEAD" and updating file paths).

    code diff:

    -5. Peptide identification FDR [`openms fdr tool`](https://github.com/bibgio/quantms/blob/dev/modules/local/openms/falsediscoveryrate/main.nf)
+5. Peptide identification FDR [`openms fdr tool`](https://github.com/bigbio/quantms/blob/HEAD/modules/local/openms/false_discovery_rate/main.nf)
 6. Modification localization [`luciphor`](https://github.com/dfermin/lucXor)
 7. Quantification: Feature detection [`proteomicsLFQ`](https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_ProteomicsLFQ.html)
 8. Protein inference and quantification [`proteomicsLFQ`](https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_ProteomicsLFQ.html)
@@ -47,7 +47,7 @@
 2. Peptide identification using [`comet`](https://uwpr.github.io/Comet/) and/or [`msgf+`](https://github.com/MSGFPlus/msgfplus)
 3. (Optional) Add extra PSM features using [`ms2rescore`](https://github.com/compomics/ms2rescore)
 4. Re-scoring peptide identifications [`percolator`](https://github.com/percolator/percolator)
-5. Peptide identification FDR [`openms fdr tool`](https://github.com/bigbio/quantms/blob/dev/modules/local/openms/falsediscoveryrate/main.nf)
+5. Peptide identification FDR [`openms fdr tool`](https://github.com/bigbio/quantms/blob/HEAD/modules/local/openms/false_discovery_rate/main.nf)

    The GitHub repository URL appears to have a typo. Based on the context and other
    links in the file, this should likely be "bigbio" instead of "bibgio".

    README.md [37]

    -5. Peptide identification FDR [`openms fdr tool`](https://github.com/bibgio/quantms/blob/dev/modules/local/openms/falsediscoveryrate/main.nf)
+5. Peptide identification FDR [`openms fdr tool`](https://github.com/bigbio/quantms/blob/dev/modules/local/openms/falsediscoveryrate/main.nf)

    [Suggestion processed]

    Suggestion importance[1-10]: 7

    __

    Why: The suggestion correctly identifies a typo in a GitHub URL where bibgio should be bigbio. This fixes a broken link in the documentation that was introduced in this PR.

    		Medium
    • Update

    @ypriverol ypriverol self-requested a review July 17, 2025 11:33
    @ypriverol ypriverol merged commit 2e3af55 into dev Jul 17, 2025
    20 of 22 checks passed
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