Data

Tools

Indexes

Applications

Experiments

Open Source Science

https://github.com/broadinstitute/warp

Warp Analysis Research Pipelines

https://github.com/broadinstitute/warp

Science Score: 39.0%

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

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 2 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (11.4%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Warp Analysis Research Pipelines

Basic Info
Statistics
  • Stars: 215
  • Watchers: 23
  • Forks: 111
  • Open Issues: 13
  • Releases: 1,000
Created about 6 years ago · Last pushed 10 months ago
Metadata Files
Readme Changelog License

README.md

Warp Analysis Research Pipelines

The Warp Analysis Research Pipelines (WARP) repository is a collection of cloud-optimized pipelines for processing biological data from the Broad Institute Data Sciences Platform and collaborators.

WARP provides robust, standardized data analysis for the Broad Institute Genomics Platform and large consortia like the Human Cell Atlas and the BRAIN Initiative. WARP pipelines are rigorously scientifically validated, high scale, reproducible and open source, released under the BSD 3-Clause license.

Pipeline releases

All pipeline releases are listed on the WARP releases page. To discover and search releases, use the WARP command-line tool Wreleaser.

WARP Dockers and custom tools in warp-tools repository

All Dockers and custom tools used for WARP's WDL Workflows are maintained in a separate repository, warp-tools.

WARP documentation

Read more about our pipelines and repository on the WARP documentation site.

To contribute to WARP, please read the contribution guidelines.

Citing WARP

When citing WARP, please use the following:

Degatano, K.; Awdeh, A.; Dingman, W.; Grant, G.; Khajouei, F.; Kiernan, E.; Konwar, K.; Mathews, K.; Palis, K.; Petrillo, N.; Van der Auwera, G.; Wang, C.; Way, J.; Pipelines, W. WDL Analysis Research Pipelines: Cloud-Optimized Workflows for Biological Data Processing and Reproducible Analysis. Preprints 2024, 2024012131. https://doi.org/10.20944/preprints202401.2131.v1

Build Status

Owner

  • Name: Broad Institute
  • Login: broadinstitute
  • Kind: organization
  • Location: Cambridge, MA

Broad Institute of MIT and Harvard

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 29
  • Total pull requests: 768
  • Average time to close issues: 5 months
  • Average time to close pull requests: 22 days
  • Total issue authors: 24
  • Total pull request authors: 30
  • Average comments per issue: 3.17
  • Average comments per pull request: 11.92
  • Merged pull requests: 512
  • Bot issues: 0
  • Bot pull requests: 49
Past Year
  • Issues: 7
  • Pull requests: 458
  • Average time to close issues: 9 days
  • Average time to close pull requests: 6 days
  • Issue authors: 6
  • Pull request authors: 15
  • Average comments per issue: 5.43
  • Average comments per pull request: 13.15
  • Merged pull requests: 302
  • Bot issues: 0
  • Bot pull requests: 36
View more stats
Top Authors
Issue Authors
  • ekiernan (4)
  • meganshand (2)
  • kachulis (2)
  • zhaohongqiangsoliva (1)
  • jdidion (1)
  • nikellepetrillo (1)
  • nicholema (1)
  • innerpyg (1)
  • beneopp (1)
  • seetarajpara (1)
  • mmwheel (1)
  • vzupan3 (1)
  • johnbradley (1)
  • eprdz (1)
  • kzb193 (1)
Pull Request Authors
  • nikellepetrillo (248)
  • ekiernan (181)
  • aawdeh (83)
  • dependabot[bot] (49)
  • rsc3 (38)
  • jessicaway (36)
  • kevinpalis (20)
  • jsotobroad (18)
  • kayleemathews (17)
  • mmorgantaylor (16)
  • meganshand (12)
  • khajoue2 (9)
  • kachulis (5)
  • vsmalladi (4)
  • ldgauthier (4)
Top Labels
Issue Labels
bug (1) ticket made (1) eng-only (1)
Pull Request Labels
dependencies (49) javascript (39) DO NOT MERGE (32) eng-only (15) python (10) documentation (3)

Packages

  • Total packages: 2
  • Total downloads: unknown
  • Total dependent packages: 0
    (may contain duplicates)
  • Total dependent repositories: 0
    (may contain duplicates)
  • Total versions: 95
proxy.golang.org: github.com/broadinstitute/warp/wreleaser
  • Versions: 92
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Forks count: 2.1%
Stargazers count: 2.7%
Average: 5.3%
Dependent packages count: 7.0%
Dependent repos count: 9.3%
Last synced: 10 months ago
proxy.golang.org: github.com/broadinstitute/warp
  • Versions: 3
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 7.0%
Average: 8.2%
Dependent repos count: 9.3%
Last synced: 10 months ago

Dependencies

.github/workflows/doc_publish.yml actions
  • JamesIves/github-pages-deploy-action releases/v3 composite
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • actions/setup-node v2 composite
.github/workflows/doc_test.yml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • actions/setup-node v2 composite
.github/workflows/womtool_check.yml actions
  • actions/checkout v2 composite
pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/biobambam2/Dockerfile docker
  • ubuntu bionic-20180426 build
pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/bwa/Dockerfile docker
  • ubuntu bionic-20180426 build
pipelines/skylab/optimus/scripts/Dockerfile docker
  • python 3.7.7 build
verification/test-wdls/scripts/requirements.txt pypi
  • jinja2 ==3.1.2 test
.github/workflows/merge_reminder.yml actions
deprecated/dockers/cemba/bismark/Dockerfile docker
  • quay.io/broadinstitute/bowtie2 2.3.4.3 build
deprecated/dockers/cemba/bisulfite-references/Dockerfile docker
  • continuumio/miniconda3 4.5.11 build
deprecated/dockers/cemba/bowtie2/Dockerfile docker
  • quay.io/broadinstitute/samtools 1.9 build
deprecated/dockers/cemba/cutadapt/Dockerfile docker
  • python 2 build
deprecated/dockers/cemba/picard/Dockerfile docker
  • alpine 3.8 build
deprecated/dockers/cemba/samtools/Dockerfile docker
  • continuumio/miniconda3 4.5.11 build
deprecated/dockers/cemba/vcftoallc/Dockerfile docker
  • python 3.7.2 build
deprecated/dockers/genomes_on_the_cloud/Dockerfile docker
  • us.gcr.io/broad-dsp-gcr-public/base/jre 8-debian build
tests/broad/scala_test/src/main/resources/clio/docker-compose.yml docker