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Visium HD support #101

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@cavenel cavenel commented Dec 20, 2024 •
edited by fasterius
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This PR adds support for Visium HD slides.

  • Update metro map with Visium HD

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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 03a20db

+| ✅ 179 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   6 tests had warnings |!

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  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
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    \n \n <source media="(prefers-color-scheme: dark)" srcset="docs/images/nf-core-spatialvi_logo_dark.png">\n <img alt="nf-core/spatialvi" src="docs/images/nf-core-spatialvi_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\nnf-core/spatialvi 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/spatialvi \\\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/spatialvi was originally written by Erik Fasterius, Christophe Avenel, Sergii Domanskyi, Jeffrey Chuang, Anuj Srivastava.\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 #spatialvi 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/spatialvi 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",
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Run details

  • nf-core/tools version 3.1.1
  • Run at 2025-02-07 13:04:36

@fasterius fasterius linked an issue Dec 20, 2024 that may be closed by this pull request
Add compatibility for Visium HD #95
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nf-core-bot commented Jan 10, 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: 3.1.1.
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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sebotic commented Jan 29, 2025 •
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On the Visium HD flag, wouldn't it be more convenient using the slide serial number prefix to determine Visium version instead of requiring a dedicated flag? Prefixes are defined here, would be "H1" for current version of Visium HD.

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cavenel commented Jan 31, 2025

On the Visium HD flag, wouldn't it be more convenient using the slide serial number prefix to determine Visium version instead of requiring a dedicated flag? Prefixes are defined here, would be "H1" for current version of Visium HD.

So you mean that we remove the --visium_hd flag, and instead rely on the first one or two characters of the slide column in the input csv?
That's an option indeed. But if we take the first two digits, then the pipeline won't work when 10X starts making H2, even if they keep backward compatibility. What would be the best approach? @fasterius do you have an opinion on this?

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If we can read the correct parameters from the samplesheet that's great, as long as it doesn't introduce issues with misidentifying anything. Regarding backwards compatibility, why wouldn't the pipeline work anymore when 10X starts making H2? If we're matching for H1 we can also match for H2 or HN, no?

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cavenel commented Jan 31, 2025

If we're matching for H1 we can also match for H2 or HN, no?

Definitely, I was more thinking that it means updating the pipeline at each new version, but that's probably needed anyway to update SR versions etc. So yes sounds like a good idea to check Visium version from slide id!

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cavenel commented Feb 7, 2025

I now removed the --visium_hd flag in dd9a8ba
For downstream analysis, as we do not give "slide" parameter, I use the existence of a "binned_outputs" folder in the SpaceRanger output.

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Add compatibility for Visium HD
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@cavenel @nf-core-bot @sebotic @fasterius