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quantms-rescoring 0.0.6 #498

Merged
merged 2 commits into from
Mar 23, 2025
Merged

quantms-rescoring 0.0.6 #498

merged 2 commits into from
Mar 23, 2025

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ypriverol
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@ypriverol ypriverol commented Mar 21, 2025 •
edited by qodo-merge-pro bot
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PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/quantms branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

PR Type

enhancement, configuration changes

Description

  • Updated quantms-rescoring dependency from version 0.0.5 to 0.0.6.

  • Adjusted conda and container configurations in ms2rescore module.

Changes walkthrough 📝

Relevant files
Documentation
CHANGELOG.md
Update changelog for `quantms-rescoring` version bump       

CHANGELOG.md

  • Updated quantms-rescoring version from 0.0.5 to 0.0.6 in the
    changelog.
    		• +1/-1     
    Configuration changes
    main.nf
    Update `ms2rescore` module for `quantms-rescoring` 0.0.6 

    modules/local/ms2rescore/main.nf

  • Updated conda configuration to use quantms-rescoring version 0.0.6.
  • Updated container URLs to reflect version 0.0.6.
    		• +3/-3     
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  • Type /help how to ... in the comments thread for any questions about Qodo Merge usage.
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    github-actions bot commented Mar 21, 2025 •
    edited
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    nf-core pipelines lint overall result: Passed ✅ ⚠️

    Posted for pipeline commit 9621c26

    +| ✅ 105 tests passed       |+
#| ❔  13 tests were ignored |#
!| ❗  26 tests had warnings |!

    ❗ 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 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 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 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 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 base.config: Check the defaults for all processes
    • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
    • local_component_structure - preprocess_expdesign.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
    • local_component_structure - samplesheet_check.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
    • local_component_structure - featuremapper.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
    • local_component_structure - create_input_channel.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
    • local_component_structure - proteininference.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
    • local_component_structure - databasesearchengines.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
    • local_component_structure - proteinquant.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
    • local_component_structure - dda_id.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
    • local_component_structure - phosphoscoring.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
    • local_component_structure - file_preparation.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
    • local_component_structure - psmrescoring.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
    • local_component_structure - id.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
    • local_component_structure - input_check.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
    • local_component_structure - psmfdrcontrol.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

    ❔ Tests ignored:

    ✅ Tests passed:

    Run details

    • nf-core/tools version 3.2.0
    • Run at 2025-03-21 19:49:15

    @ypriverol ypriverol requested a review from daichengxin March 22, 2025 15:01
    @ypriverol ypriverol merged commit 41e9539 into bigbio:dev Mar 23, 2025
    86 of 90 checks passed
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    @daichengxin daichengxin daichengxin approved these changes

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    @ypriverol @daichengxin