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major change to run CI on dev using dev conf #464

Merged
merged 14 commits into from
Dec 23, 2024
Merged

major change to run CI on dev using dev conf #464

merged 14 commits into from
Dec 23, 2024

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ypriverol
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@ypriverol ypriverol commented Dec 20, 2024 •
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This PR is the first step to start synchronising quantms with the release cycle of OpenMS #463. Here, the dev branch of quantms will be using the latest version of OpenMS containers.

In summary, The ci.yml will test both master & dev, if the PR is against dev branch, then we will be using the latest containers from OpenMS and Singularity; if the PR is against the master, then we will be using conda, singularity and docker with the latest release of OpenMS.

ProteinInference should always make sure that will be using the PEP score: -Algorithm:score_type "PEP"

In addition, this PR includes a new change for big DIA datasets that mzTab export doesn't scale, to export only the msstats input file.

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).

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github-actions bot commented Dec 20, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 80a84aa

+| ✅ 104 tests passed       |+
#| ❔  13 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

    GitHub 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 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 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 ci.yml: You can customise CI pipeline run tests as required
  • pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run tests as required
  • 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.

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.1.1
  • Run at 2024-12-23 08:29:27

@ypriverol
Template update for nf-core/tools version 3.1.0
d7d4b74
@ypriverol
Merge branch 'TEMPLATE' into dev
417b174 
# Conflicts:
#	.github/CONTRIBUTING.md
#	.github/workflows/awsfulltest.yml
#	.github/workflows/awstest.yml
#	.github/workflows/ci.yml
#	CHANGELOG.md
#	README.md
#	assets/multiqc_config.yml
#	conf/test.config
#	conf/test_full.config
#	docs/usage.md
#	main.nf
#	nextflow.config
@ypriverol
template 3.1.0 update
1ebbef0
@ypriverol
Template update for nf-core/tools version 3.1.1
c6d8091
@ypriverol
Merge branch 'TEMPLATE' into dev
6ed3398 
# Conflicts:
#	.prettierignore
#	CITATIONS.md
#	README.md
#	docs/output.md
#	docs/usage.md
#	subworkflows/local/utils_nfcore_quantms_pipeline/main.nf
@ypriverol
template 3.1.0 update
5a70360
@ypriverol
template 3.1.0 update
f226734
@ypriverol
template 3.1.0 update
a2e4a66
@ypriverol
ProteinInference new parameter.
b45716a
@ypriverol
Make DIANN to mzTab optional
054d906
@ypriverol
Make DIANN to mzTab optional
012c54f
@ypriverol
Make DIANN to mzTab optional, template 3.1.0, bug fixing
eed4670
@ypriverol
Merge remote-tracking branch 'origin/dev' into dev
80a84aa
@ypriverol ypriverol requested review from daichengxin and jpfeuffer and removed request for daichengxin December 23, 2024 08:30
@ypriverol ypriverol merged commit 70337bc into bigbio:dev Dec 23, 2024
21 checks passed
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@daichengxin daichengxin daichengxin approved these changes

@jpfeuffer jpfeuffer Awaiting requested review from jpfeuffer

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@ypriverol @daichengxin