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Add long reads #109

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@TMAdams TMAdams commented Mar 26, 2025 •
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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/seqinspector 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). [reports no tests to execute]
  • 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).

This PR adds toulligqc as an optional component for QC of long reads.

TODO:

  • Get toulligqc to interface with multiqc -> may require an extension to multiqc
  • Tests likely need to be added

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github-actions bot commented Mar 26, 2025 •
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nf-core pipelines lint overall result: Failed ❌

Posted for pipeline commit ee0f4e5

+| ✅ 194 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗  16 tests had warnings |!
-| ❌   1 tests failed       |-

❌ Test failures:

  • multiqc_config - assets/multiqc_config.yml does not contain a matching 'report_comment'.
    The expected comment is:
    This report has been generated by the <a href="https://github.com/nf-core/seqinspector/tree/dev" target="_blank">nf-core/seqinspector</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/seqinspector/dev/docs/output" target="_blank">documentation</a>.
    The current comment is:
    This report has been generated by the <a href="https://github.com/nf-core/seqinspector/tree/dev" target="_blank">nf-core/seqinspector</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/seqinspector/dev/docs/output" target="_blank">documentation</a>. If ToulligQC was used, a separate report is available in the results folder.

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in nextflow.config: Specify your pipeline's command line flags
  • 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 README.md: TODO nf-core:
  • pipeline_todos - TODO string in README.md: Include a figure that guides the user through the major workflow steps. Many nf-core
  • pipeline_todos - TODO string in README.md: Fill in short bullet-pointed list of the default steps in the pipeline
  • 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 main.nf: Remove this line if you don't need a FASTA file
  • pipeline_todos - TODO string in ro-crate-metadata.json: "description": "

    \n \n <source media="(prefers-color-scheme: dark)" srcset="docs/images/nf-core-seqinspector_logo_dark.png">\n <img alt="nf-core/seqinspector" src="docs/images/nf-core-seqinspector_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/seqinspector 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 nf-core/seqinspector \\\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/seqinspector was originally written by Adrien Coulier.\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 #seqinspector 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/seqinspector 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 test.config: Specify the paths to your test data on nf-core/test-datasets
  • pipeline_todos - TODO string in test.config: Give any required params for the test so that command line flags are not needed
  • 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.
  • pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md

✅ Tests passed:

Run details

  • nf-core/tools version 3.2.0
  • Run at 2025-03-26 15:27:31

@FranBonath
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FranBonath commented Mar 26, 2025 •
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ok, so. If there is no multiqc module for toulligqc, then the only way to get info into the multiqc report is via custom content. For that to work, you need to have the output in some sort of machine readable form, but the main point is, that you just append *_mqc to the end of the file name (and before the extension I believe) and multiqc will recognize it.

@TMAdams
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TMAdams commented Mar 26, 2025

Okay, there is a text output, let me see if I can make it behave

mahesh-panchal
mahesh-panchal reviewed Mar 26, 2025
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workflows/seqinspector.nf Outdated
TOULLIGQC (
ch_samplesheet
)
ch_multiqc_files.mix(TOULLIGQC.out)
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@mahesh-panchal mahesh-panchal Mar 26, 2025

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This is taking all the output channels of TOULLIGQC. Is that what you want?

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@TMAdams TMAdams Mar 26, 2025

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Possibly not. There's a plaintext .data file which might be able to go into multiqc, I'll need to look into if there's a way to split out just that tuple from the output

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Suggested change
ch_multiqc_files.mix(TOULLIGQC.out)
ch_multiqc_files.mix(TOULLIGQC.out.report_data)

Then you just want that channel I think.

MQC doesn't list TOULLIGQC, but if it produces an output suitable for it, then you can add it in a custom content section.

custom_data:
  dtol:
    file_format: "tsv"
    section_name: "DToL"
    description: "Darwin Tree of Life identifier and related meta data."
    plot_type: "table"
sp: # Search pattern
  dtol:
    fn: "DToL.tsv"

See https://docs.seqera.io/multiqc/custom_content for more info

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@TMAdams TMAdams Mar 26, 2025

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Fab ty! I'll give it a shot 🤞

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TMAdams commented Mar 26, 2025

Made some attempts to pass the QC results as custom, couldn't get it to work. I think we want to get a module for toulligqc in multiqc in the long term. So for now I just signpost users to the html report from toulligqc

@TMAdams TMAdams marked this pull request as ready for review March 26, 2025 14:59
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@TMAdams @FranBonath @mahesh-panchal