diff --git a/.gitattributes b/.gitattributes index 7a2dabc..31ba574 100644 --- a/.gitattributes +++ b/.gitattributes @@ -2,3 +2,4 @@ *.nf.test linguist-language=nextflow modules/nf-core/** linguist-generated subworkflows/nf-core/** linguist-generated +tests/**/*nf.test.snap linguist-generated diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index a5e811f..6972735 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -5,11 +5,16 @@ on: branches: - dev pull_request: + branches: + - dev + - master release: types: [published] env: NXF_ANSI_LOG: false + CAPSULE_LOG: none + NFTEST_VER: "0.7.3" concurrency: group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" @@ -22,25 +27,38 @@ jobs: if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/spatialvi') }}" runs-on: ubuntu-latest strategy: + fail-fast: false matrix: NXF_VER: - "23.04.0" - "latest-everything" + test: + - tests/pipeline/test_spaceranger_ffpe_v1.nf.test + - tests/pipeline/test_spaceranger_ffpe_v2_cytassist.nf.test + - tests/pipeline/test_downstream.nf.test steps: - name: Check out pipeline code uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + # Install Nextflow - name: Install Nextflow uses: nf-core/setup-nextflow@v2 with: version: "${{ matrix.NXF_VER }}" - - name: Disk space cleanup - uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 + # Install nf-test + - name: Install nf-test + run: | + wget -qO- https://code.askimed.com/install/nf-test | bash -s $NFTEST_VER + sudo mv nf-test /usr/local/bin/ + + # Run nf-test + - name: Run nf-test + run: nf-test test --profile=test,docker --tap=test.tap ${{ matrix.test }} - - name: Run pipeline with test data - # TODO nf-core: You can customise CI pipeline run tests as required - # For example: adding multiple test runs with different parameters - # Remember that you can parallelise this by using strategy.matrix + # If the test fails, output the software_versions.yml using the 'batcat' utility + - name: Output log on failure + if: failure() run: | - nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results + sudo apt install bat > /dev/null + batcat --decorations=always --color=always .nf-test/tests/*/output/pipeline_info/software_versions.yml diff --git a/.gitignore b/.gitignore index 5124c9a..0699257 100644 --- a/.gitignore +++ b/.gitignore @@ -6,3 +6,9 @@ results/ testing/ testing* *.pyc +log +reports +.nf-test/ +nf-test +.nf-test* +test-datasets diff --git a/.nf-core.yml b/.nf-core.yml index e0b85a7..0697501 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1,2 +1,11 @@ repository_type: pipeline nf_core_version: "2.14.1" +lint: + actions_ci: False + files_exist: + - conf/igenomes.config + files_unchanged: + - .gitattributes + - assets/nf-core-spatialvi_logo_light.png + - docs/images/nf-core-spatialvi_logo_light.png + - docs/images/nf-core-spatialvi_logo_dark.png \ No newline at end of file diff --git a/.prettierignore b/.prettierignore index 437d763..dd856fc 100644 --- a/.prettierignore +++ b/.prettierignore @@ -10,3 +10,6 @@ testing/ testing* *.pyc bin/ +test-datasets/ +.nf-test/ +*.scss diff --git a/CHANGELOG.md b/CHANGELOG.md index 7af7cd7..84cc97d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,14 +3,67 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## v1.0dev - [date] +## [Unreleased] -Initial release of nf-core/spatialvi, created with the [nf-core](https://nf-co.re/) template. +Initial release of nf-core/spatialvi, created with the +[nf-core](https://nf-co.re/) template. This marks the point at which the +pipeline development was moved to nf-core and NBIS. The pipeline has undergone +several iterations regarding its functionality and content; there are a +significant number of changes, of which not all are listed here. In summary, the +pipeline contains best-practice processing and analyses of pre- and post-Space +Ranger-processed data, including quality controls, normalisation, dimensionality +reduction, clustering, differential expression testing as well as output files +compatible with further downstream analyses and/or exploration in _e.g._ +[TissUUmaps](https://tissuumaps.github.io/) or bespoke user code. ### `Added` +- Add MultiQC support for Space Ranger outputs [[#70](https://github.com/nf-core/spatialvi/pull/70)] +- Use the QUARTONOTEBOOK nf-core module instead of local Quarto-based modules [[#68](https://github.com/nf-core/spatialvi/pull/68)] +- Add support for SpatialData [[$67](https://github.com/nf-core/spatialvi/pull/67)] +- Add a custom nf-core Quarto template for the downstream analysis reports [[#64](https://github.com/nf-core/spatialvi/pull/64)] +- Allow input directories `fastq_dir` and `spaceranger_dir` to be specified as tar archives (`.tar.gz`) +- Add a check to make sure that there are spots left after filtering [[#46](https://github.com/nf-core/spatialvi/issues/46)] +- Implement tests with nf-test [[#42](https://github.com/nf-core/spatialvi/pull/42)] +- Replace custom code to download reference with `untar` module [[#44](https://github.com/nf-core/spatialvi/pull/44)] +- Embed resources in quarto reports [[#43](https://github.com/nf-core/spatialvi/pull/43)] +- Use a samplesheet for input specification [[#30](https://github.com/nf-core/spatialvi/pull/30), [#31](https://github.com/nf-core/spatialvi/pull/31) and [#45](https://github.com/nf-core/spatialvi/pull/45)] +- Add Space Ranger pre-processing as an optional pipeline step using the `spaceranger` nf-core module [[#17](https://github.com/nf-core/spatialvi/pull/17) and [#45](https://github.com/nf-core/spatialvi/pull/45)] +- Add `env/` directory with pipeline-specific container and Conda environment specifications [[#17](https://github.com/nf-core/spatialvi/pull/17) and [#28](https://github.com/nf-core/spatialvi/pull/28)] +- Use a more standardised practice to find mitochondrial genes [[#30](https://github.com/nf-core/spatialvi/pull/30)] +- Make pipeline output compatible with TissUUmaps [[#31](https://github.com/nf-core/spatialvi/pull/31)] +- Add custom Quarto-based reports for all downstream processing [[#31](https://github.com/nf-core/spatialvi/pull/31)] +- Embed resources in quarto reports [[#43](https://github.com/nf-core/spatialvi/pull/43)] + ### `Fixed` +- [#51](https://github.com/nf-core/spatialvi/issues/51): Fix version export of `leidenalg` and `SpatialDE` Python modules +- [#38](https://github.com/nf-core/spatialvi/issues/38): Specify manual alignment files in samplesheet +- [#20](https://github.com/nf-core/spatialvi/issues/20) and [#22](https://github.com/nf-core/spatialvi/issues/22): Add missing Groovy module +- [#53](https://github.com/nf-core/spatialvi/pull/53): Use ensemble IDs as index in adata.var and fix related + issue with SpatialDE + ### `Dependencies` -### `Deprecated` +Note, since the pipeline is using Nextflow DSL2, each process will be run +with its own [Biocontainer](https://biocontainers.pro/#/registry). This means +that on occasion it is entirely possible for the pipeline to be using different +versions of the same tool. + +| Dependency | Version | +| ----------- | ------- | +| `SpatialDE` | 1.1.3 | +| `leidenalg` | 0.9.1 | +| `python` | 3.12.0 | +| `quarto` | 1.3.302 | +| `scanpy` | 1.9.3 | + +### `Removed` + +- Streamline pipeline for basic ST data processing; remove SC processing and deconvolution (for now) [[#31](https://github.com/nf-core/spatialvi/pull/31)] + +## v0.1.0 - 2023-03-31 + +Initial release of nf-core/spatialvi, created with the +[nf-core](https://nf-co.re/) template by the Jackson Laboratory contributors +(see `README.md` for details). diff --git a/CITATIONS.md b/CITATIONS.md index b15a7c6..5f048a5 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -10,6 +10,10 @@ ## Pipeline tools +- [AnnData](https://github.com/scverse/anndata) + + > Virshup I, Rybakov S, Theis FJ, Angerer P, Wolf FA. bioRxiv 2021.12.16.473007; doi: https://doi.org/10.1101/2021.12.16.473007 + - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. @@ -18,6 +22,26 @@ > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. +- [Quarto](https://quarto.org/) + + > Allaire J, Teague C, Scheidegger C, Xie Y, Dervieux C. Quarto (2022). doi: 10.5281/zenodo.5960048 + +- [Scanpy](https://github.com/theislab/scanpy) + + > Wolf F, Angerer P, Theis F. SCANPY: large-scale single-cell gene expression data analysis. Genome Biol 19, 15 (2018). doi: https://doi.org/10.1186/s13059-017-1382-0 + +- [Space Ranger](https://www.10xgenomics.com/support/software/space-ranger) + + > 10x Genomics Space Ranger 2.1.0 [Online] + +- [SpatialData](https://www.biorxiv.org/content/10.1101/2023.05.05.539647v1) + + > Marconato L, Palla G, Yamauchi K, Virshup I, Heidari E, Treis T, Toth M, Shrestha R, Vöhringer H, Huber W, Gerstung M, Moore J, Theis F, Stegle O. SpatialData: an open and universal data framework for spatial omics. bioRxiv 2023.05.05.539647; doi: https://doi.org/10.1101/2023.05.05.539647 + +- [Squipy](https://www.nature.com/articles/s41592-021-01358-2) + + > Palla G, Spitzer H, Klein M et al. Squidpy: a scalable framework for spatial omics analysis. Nat Methods 19, 171–178 (2022). doi: https://doi.org/10.1038/s41592-021-01358-2 + ## Software packaging/containerisation tools - [Anaconda](https://anaconda.com) diff --git a/README.md b/README.md index b7a0472..637d261 100644 --- a/README.md +++ b/README.md @@ -19,45 +19,45 @@ ## Introduction -**nf-core/spatialvi** is a bioinformatics pipeline that ... - - - - - - -1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)) -2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/)) +**nf-core/spatialvi** is a bioinformatics analysis pipeline for Visium spatial +transcriptomics data from 10x Genomics. It can process and analyse spatial data +either directly from raw data by running [Space Ranger](https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger) +or data already processed by Space Ranger. The pipeline currently consists of +the following steps: + +

+ +

+ +0. Raw data processing with Space Ranger (optional) +1. Quality controls and filtering +2. Normalisation +3. Dimensionality reduction and clustering +4. Differential gene expression testing + +The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool +to run tasks across multiple compute infrastructures in a very portable manner. +It uses Docker/Singularity containers making installation trivial and results +highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) +implementation of this pipeline uses one container per process which makes it +much easier to maintain and update software dependencies. Where possible, these +processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) +in order to make them available to all nf-core pipelines, and to everyone within +the Nextflow community! + +On release, automated continuous integration tests run the pipeline on a +full-sized dataset on the AWS cloud infrastructure. This ensures that the +pipeline runs on AWS, has sensible resource allocation defaults set to run on +real-world datasets, and permits the persistent storage of results to benchmark +between pipeline releases and other analysis sources. The results obtained from +the full-sized test can be viewed on the [nf-core website](https://nf-co.re/spatialvi/results). ## Usage > [!NOTE] > If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data. - - -Now, you can run the pipeline using: - - +You can run the pipeline using: ```bash nextflow run nf-core/spatialvi \ @@ -67,8 +67,7 @@ nextflow run nf-core/spatialvi \ ``` > [!WARNING] -> 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](https://nf-co.re/usage/configuration#custom-configuration-files). +> 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](https://nf-co.re/usage/configuration#custom-configuration-files). For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/spatialvi/usage) and the [parameter documentation](https://nf-co.re/spatialvi/parameters). @@ -80,11 +79,22 @@ For more details about the output files and reports, please refer to the ## Credits -nf-core/spatialvi was originally written by Erik Fasterius, Christophe Avenel, Sergii Domanskyi, Jeffrey Chuang, Anuj Srivastava. +nf-core/spatialvi was originally developed by the Jackson +Laboratory1, up to the [0.1.0](https://github.com/nf-core/spatialvi/releases/tag/0.1.0) +tag. It was further developed in a collaboration between the [National +Bioinformatics Infrastructure Sweden](https://nbis.se/) and [National Genomics +Infrastructure](https://ngisweden.scilifelab.se/) within [SciLifeLab](https://scilifelab.se/); +it is currently developed and maintained by [Erik Fasterius](https://github.com/fasterius) +and [Christophe Avenel](https://github.com/cavenel). -We thank the following people for their extensive assistance in the development of this pipeline: +Many thanks to others who have helped out along the way too, especially [Gregor +Sturm](https://github.com/grst)! - +_1 Supported by grants from the US National Institutes of Health +[U24CA224067](https://reporter.nih.gov/project-details/10261367) and +[U54AG075941](https://reporter.nih.gov/project-details/10376627). Original +authors [Dr. Sergii Domanskyi](https://github.com/sdomanskyi), Prof. Jeffrey +Chuang and Dr. Anuj Srivastava._ ## Contributions and Support @@ -97,8 +107,6 @@ For further information or help, don't hesitate to get in touch on the [Slack `# - - An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file. You can cite the `nf-core` publication as follows: diff --git a/assets/_extensions/nf-core/_extension.yml b/assets/_extensions/nf-core/_extension.yml new file mode 100644 index 0000000..95759fc --- /dev/null +++ b/assets/_extensions/nf-core/_extension.yml @@ -0,0 +1,25 @@ +title: nf-core Quarto Extension +author: Erik Fasterius +version: 1.0.0 +quarto-required: ">=1.2.0" +contributes: + formats: + html: + code-fold: true + df-print: paged + embed-resources: true + highlight-style: nf-core.theme + smooth-scroll: true + theme: [default, nf-core.scss] + toc: true + toc-image: nf-core-spatialvi_logo_light.png + toc-location: left + template-partials: + - toc.html + revealjs: + code-line-numbers: false + embed-resources: true + logo: nf-core-spatialvi_logo_light.png + slide-level: 2 + slide-number: false + theme: [default, nf-core.scss] diff --git a/assets/_extensions/nf-core/nf-core-spatialvi_logo_light.png b/assets/_extensions/nf-core/nf-core-spatialvi_logo_light.png new file mode 120000 index 0000000..b20f5fe --- /dev/null +++ b/assets/_extensions/nf-core/nf-core-spatialvi_logo_light.png @@ -0,0 +1 @@ +../../nf-core-spatialvi_logo_light.png \ No newline at end of file diff --git a/assets/_extensions/nf-core/nf-core.scss b/assets/_extensions/nf-core/nf-core.scss new file mode 100644 index 0000000..788a029 --- /dev/null +++ b/assets/_extensions/nf-core/nf-core.scss @@ -0,0 +1,194 @@ +/*-- scss:defaults --*/ + +$theme: "nf-core" !default; + +// Colours +$green: #24B064 !default; +$blue: #3073AF !default; +$red: #E0191A !default; +$yellow: #DABC25 !default; + +// Greyscale +$white: #FFFFFF !default; +$grey-100: #F5F5F5 !default; +$grey-90: #E5E5E5 !default; +$grey-80: #CCCCCC !default; +$grey-70: #B2B2B2 !default; +$grey-60: #999999 !default; +$grey-50: #7F7F7F !default; +$grey-40: #666666 !default; +$grey-30: #4C4C4C !default; +$grey-20: #333333 !default; +$grey-10: #191919 !default; +$black: #000000 !default; + +// Theme +$primary: $green !default; +$secondary: $blue 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false, + "italic": false, + "underline": false + }, + "Keyword": { + "text-color": "#BB5454 ", + "background-color": null, + "bold": true, + "italic": false, + "underline": false + } + } +} diff --git a/assets/_extensions/nf-core/toc.html b/assets/_extensions/nf-core/toc.html new file mode 100644 index 0000000..b402642 --- /dev/null +++ b/assets/_extensions/nf-core/toc.html @@ -0,0 +1,7 @@ + diff --git a/assets/methods_description_template.yml b/assets/methods_description_template.yml index b4c018f..11102b9 100644 --- a/assets/methods_description_template.yml +++ b/assets/methods_description_template.yml @@ -3,7 +3,6 @@ description: "Suggested text and references to use when describing pipeline usag section_name: "nf-core/spatialvi Methods Description" section_href: "https://github.com/nf-core/spatialvi" plot_type: "html" -## TODO nf-core: Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline ## You inject any metadata in the Nextflow '${workflow}' object data: |

Methods

@@ -12,13 +11,7 @@ data: | 
${workflow.commandLine}

${tool_citations}

References

- +
Notes: