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webatlas-pipeline

A data pipeline built in Nextflow to process spatial and single-cell experiment data for visualisation in WebAtlas

https://github.com/haniffalab/webatlas-pipeline

Science Score: 67.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 3 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (11.1%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

A data pipeline built in Nextflow to process spatial and single-cell experiment data for visualisation in WebAtlas

Basic Info
  • Host: GitHub
  • Owner: haniffalab
  • License: mit
  • Language: Python
  • Default Branch: main
  • Homepage:
  • Size: 6.22 MB
Statistics
  • Stars: 64
  • Watchers: 6
  • Forks: 10
  • Open Issues: 21
  • Releases: 11
Created about 4 years ago · Last pushed 8 months ago
Metadata Files
Readme License Citation

README.md

python-tests codecov

WebAtlas Pipeline

docs demo doi

The WebAtlas Pipeline uses Nextflow to process spatial and single-cell experiment data for visualisation in a web browser.

Usage

The pipeline can handle data from h5ad files, tif image files, SpaceRanger, Xenium and MERSCOPE output. It can also generate label image files from data files.

Running the pipeline requires a parameters file that defines configuration options and the data to be processed. Full instructions and parameters definitions for this files are available in the documentation

A parameters file looks like:

```yaml outdir: "/path/to/output/"

args: h5ad: compute_embeddings: "True"

projects: - project: project1 datasets: - dataset: dataset1 data: - datatype: h5ad datapath: /path/to/project1/dataset1/anndata.h5ad - datatype: rawimage datapath: /path/to/project1/dataset1/rawimage.tif - datatype: labelimage datapath: /path/to/project1/dataset1/labelimage.tif

vitessceoptions: spatial: xy: "obsm/spatial" mappings: obsm/Xumap: [0, 1] layout: "simple" ```

The pipeline can then be run like:

sh nextflow run main.nf -params-file /path/to/run-params.yaml -entry Full_pipeline

Parameters file templates are available in the templates directory.

Owner

  • Name: Haniffa Lab
  • Login: haniffalab
  • Kind: organization
  • Location: Newcastle upon Tyne

Based in the Newcastle University Biosciences Institute, we apply disruptive techniques to understand how the immune system develops and maintains health

Citation (CITATION.cff) 

cff-version: 1.2.0
type: software
message: "If you use this repo, please cite it"
title: "WebAtlas"
url: "https://github.com/haniffalab/webatlas-pipeline"
doi: 10.5281/zenodo.7405818
authors:
  - family-names: "Li"
    given-names: "Tong"
    orcid: "https://orcid.org/0000-0002-8240-4476"
  - family-names: "Horsfall"
    given-names: "David"
    orcid: "https://orcid.org/0000-0002-8086-812X"
  - family-names: "Basurto-Lozada"
    given-names: "Daniela"
    orcid: "https://orcid.org/0000-0003-3943-8424"
  - family-names: "Prete"
    given-names: "Martin"
    orcid: "https://orcid.org/0000-0002-5946-821X"
  - family-names: "Jessica"
    given-names: "Cox"
    orcid: "https://orcid.org/0000-0002-1109-1679"
  - family-names: "Iolo"
    given-names: "Squires"
    orcid: "https://orcid.org/0000-0002-3424-6354"

GitHub Events

Total
  • Create event: 4
  • Release event: 1
  • Issues event: 5
  • Watch event: 18
  • Delete event: 3
  • Member event: 2
  • Issue comment event: 4
  • Push event: 62
  • Pull request review event: 5
  • Pull request review comment event: 22
  • Pull request event: 7
  • Fork event: 3
Last Year
  • Create event: 4
  • Release event: 1
  • Issues event: 5
  • Watch event: 18
  • Delete event: 3
  • Member event: 2
  • Issue comment event: 4
  • Push event: 62
  • Pull request review event: 5
  • Pull request review comment event: 22
  • Pull request event: 7
  • Fork event: 3

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 2
  • Total pull requests: 3
  • Average time to close issues: N/A
  • Average time to close pull requests: about 2 hours
  • Total issue authors: 2
  • Total pull request authors: 2
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 2
  • Pull requests: 3
  • Average time to close issues: N/A
  • Average time to close pull requests: about 2 hours
  • Issue authors: 2
  • Pull request authors: 2
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • ashishjain1988 (7)
  • BioinfoTongLI (1)
  • jessica-cox (1)
  • prete (1)
  • uush99 (1)
Pull Request Authors
  • dannda (7)
  • StasMakarchuk (2)
  • datasome (2)
  • davehorsfall (1)
  • chunhuicai (1)
  • prete (1)
Top Labels
Issue Labels
Pull Request Labels

Dependencies

docker/requirements.txt pypi
  • PyYAML ==6.0
  • Shapely ==1.8.0
  • anndata ==0.8.0
  • apeer-ometiff-library ==1.8.2
  • asciitree ==0.3.3
  • cached-property ==1.5.2
  • cloudpickle ==2.0.0
  • dask ==2022.2.0
  • fasteners ==0.17.3
  • fire ==0.4.0
  • fsspec ==2022.1.0
  • h5py ==3.6.0
  • importlib-metadata ==4.11.1
  • locket ==0.2.1
  • natsort ==8.1.0
  • numcodecs ==0.9.1
  • numpy ==1.21.5
  • packaging ==21.3
  • pandas ==1.3.5
  • partd ==1.2.0
  • pyparsing ==3.0.7
  • python-dateutil ==2.8.2
  • pytz ==2021.3
  • scipy ==1.7.3
  • six ==1.16.0
  • tifffile ==2021.11.2
  • toolz ==0.11.2
  • typing-extensions ==4.1.1
  • xlrd ==1.2.0
  • zarr ==2.11.0
  • zipp ==3.7.0
.github/workflows/sphinx-build.yml actions
  • JamesIves/github-pages-deploy-action v4.4.1 composite
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
.github/workflows/tests-python.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
  • codecov/codecov-action v3 composite
docker/Dockerfile docker
  • python 3.9-slim build