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Update nf-core odgi modules to version 0.9.0 #233

Merged
merged 8 commits into from
Jan 28, 2025
Merged

Update nf-core odgi modules to version 0.9.0 #233

merged 8 commits into from
Jan 28, 2025

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heuermh
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@heuermh heuermh commented Jan 23, 2025 •
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Fixes #214
Fixes #217

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/pangenome branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nf-test test main.nf.test -profile test,docker).
  • 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 Jan 23, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 08e0e73

+| ✅ 232 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   6 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: conf/igenomes_ignored.config
  • pipeline_todos - TODO string in ro-crate-metadata.json: "description": "

    \n \n <source media="(prefers-color-scheme: dark)" srcset="docs/images/nf-core-pangenome_logo_dark.png">\n <img alt="nf-core/pangenome" src="docs/images/nf-core-pangenome_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\nnf-core/pangenome 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 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 nf-core/pangenome \\\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\nnf-core/pangenome was originally written by Simon Heumos, Michael L Heuer.\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 #pangenome 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 nf-core/pangenome 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 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!

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/nf-core-pangenome_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-pangenome_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-pangenome_logo_dark.png

✅ Tests passed:

Run details

  • nf-core/tools version 3.1.2
  • Run at 2025-01-28 08:37:36

@heuermh heuermh requested a review from subwaystation January 23, 2025 18:00
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heuermh commented Jan 23, 2025

Note commits from #223 were necessary here to pass CI for the community runs.

@heuermh heuermh mentioned this pull request Jan 23, 2025
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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.1.2.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

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Unfortunately, the ODGI table in the MultiQC report(s) is not appearing anymore with this PR. Maybe some odgi stats output changed. Will investigate.

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I just pushed a fix, the odgi stats cli changed.

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Just added -lsd and we are spaced out!

subwaystation
subwaystation approved these changes Jan 28, 2025
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LGTM!

modules/local/multiqc_community/main.nf Outdated
'https://depot.galaxyproject.org/singularity/multiqc:1.15--pyhdfd78af_0' :
'biocontainers/multiqc:1.15--pyhdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/multiqc:1.25.1--pyhdfd78af_0' :
'biocontainers/multiqc:1.25.1--pyhdfd78af_0' }"
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We need 1.26 here. My old PR did not incorporate this, because I wasn't aware of the bug.

modules/local/multiqc_community/environment.yml Outdated
- conda-forge
- bioconda
dependencies:
- bioconda::multiqc=1.25.1
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1.26

modules/local/multiqc_community/main.nf Outdated
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/multiqc:1.15--pyhdfd78af_0' :
'biocontainers/multiqc:1.15--pyhdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/multiqc:1.25.1--pyhdfd78af_0' :
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1.26

workflows/pangenome.nf
@@ -63,6 +67,11 @@ workflow PANGENOME {
)
ch_versions = ch_versions.mix(INPUT_CHECK.out.versions)
ch_multiqc_config = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true)

ch_multiqc_config = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config, checkIfExists: true) : Channel.empty()
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This line is now 3 times in this file. Please remove two instances.

workflows/pangenome.nf
@@ -63,6 +67,11 @@ workflow PANGENOME {
)
ch_versions = ch_versions.mix(INPUT_CHECK.out.versions)
ch_multiqc_config = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
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I think this line is 2 times in the file.

workflows/pangenome.nf
ch_multiqc_config = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config, checkIfExists: true) : Channel.empty()


ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config) : Channel.empty()
ch_multiqc_logo = params.multiqc_logo ? Channel.fromPath(params.multiqc_logo) : Channel.empty()
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While not introduced in this PR, this line is there 2 times, too.

@subwaystation subwaystation merged commit d22b333 into nf-core:dev Jan 28, 2025
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@heuermh @nf-core-bot @subwaystation