Data

Tools

Indexes

Applications

Experiments

Open Source Science

https://github.com/broadinstitute/viral-pipelines

viral-ngs: complete pipelines

https://github.com/broadinstitute/viral-pipelines

Science Score: 36.0%

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
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    11 of 24 committers (45.8%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (13.7%) to scientific vocabulary

Keywords from Contributors

bioinformatics metagenomics carpentries genomics
Last synced: 10 months ago · JSON representation

Repository

viral-ngs: complete pipelines

Basic Info
  • Host: GitHub
  • Owner: broadinstitute
  • License: other
  • Language: WDL
  • Default Branch: master
  • Size: 159 MB
Statistics
  • Stars: 66
  • Watchers: 13
  • Forks: 28
  • Open Issues: 41
  • Releases: 50
Created almost 7 years ago · Last pushed 11 months ago
Metadata Files
Readme License

README.md

Build Status Documentation Status

viral-pipelines

A set of scripts and tools for the analysis of viral NGS data.

Workflows are written in WDL format. This is a portable workflow language that allows for easy execution on a wide variety of platforms: - on individual machines (using miniWDL or Cromwell to execute) - on commercial cloud platforms like GCP, AWS, or Azure (using Cromwell or CromwellOnAzure) - on institutional HPC systems (using Cromwell) - on commercial platform as a service vendors (like DNAnexus) - on academic cloud platforms (like Terra)

Obtaining the latest WDL workflows

Workflows from this repository are continuously deployed to Dockstore, a GA4GH Tool Registry Service. They can then be easily imported to any bioinformatic compute platform that utilizes the TRS API and understands WDL (this includes Terra, DNAnexus, DNAstack, etc).

Workflows are also available in the Terra featured workspace.

Workflows are continuously deployed to a DNAnexus CI project.

Basic execution

The easiest way to get started is on a single, Python & Docker-capable machine (your laptop, shared workstation, or virtual machine) using miniWDL as shown above. MiniWDL can be installed either via pip or conda (via conda-forge). After confirming that it works (miniwdl run_self_test, you can use miniwdl run to invoke WDL workflows from this repository.

For example, to list the inputs for the assemble_refbased workflow:

miniwdl run https://raw.githubusercontent.com/broadinstitute/viral-pipelines/v2.1.8.0/pipes/WDL/workflows/assemble_refbased.wdl

This will emit: ``` missing required inputs for assemblerefbased: readsunmappedbams, referencefasta

required inputs: Array[File]+ readsunmappedbams File reference_fasta

optional inputs:

outputs: ```

To then execute this workflow on your local machine, invoke it with like this: miniwdl run \ https://raw.githubusercontent.com/broadinstitute/viral-ngs-staging/master/pipes/WDL/workflows/assemble_refbased.wdl \ reads_unmapped_bams=PatientA_library1.bam \ reads_unmapped_bams=PatientA_library2.bam \ reference_fasta=/refs/NC_045512.2.fasta \ trim_coords_bed=/refs/NC_045512.2-artic_primers-3.bed \ sample_name=PatientA

In the above example, reads from two sequencing runs are aligned and merged together before consensus calling. The optional bed file provided turns on primer trimming at the given coordinates.

Available workflows

The workflows provided here are more fully documented at our ReadTheDocs page.

Owner

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

Broad Institute of MIT and Harvard

GitHub Events

Total
  • Create event: 43
  • Release event: 2
  • Issues event: 4
  • Watch event: 9
  • Delete event: 34
  • Member event: 1
  • Issue comment event: 4
  • Push event: 280
  • Pull request review comment event: 8
  • Pull request review event: 14
  • Pull request event: 56
  • Fork event: 1
Last Year
  • Create event: 43
  • Release event: 2
  • Issues event: 4
  • Watch event: 9
  • Delete event: 34
  • Member event: 1
  • Issue comment event: 4
  • Push event: 280
  • Pull request review comment event: 8
  • Pull request review event: 14
  • Pull request event: 56
  • Fork event: 1

Committers

Last synced: about 1 year ago

All Time
  • Total Commits: 4,646
  • Total Committers: 24
  • Avg Commits per committer: 193.583
  • Development Distribution Score (DDS): 0.378
Past Year
  • Commits: 331
  • Committers: 4
  • Avg Commits per committer: 82.75
  • Development Distribution Score (DDS): 0.13
Top Committers
Name Email Commits
Danny Park d****k@b****g 2,889
Christopher Tomkins-Tinch t****c@b****g 1,088
Irwin Jungreis i****r@c****u 159
Simon Ye m****l@y****m 136
golu099 f****e@g****m 109
Ilya Shlyakhter i****l@a****u 52
Sushma Chaluvadi s****a@b****g 49
Lydia Andreyevna Krasilnikova l****s@m****u 45
Hayden Metsky h****y@g****m 41
Juan Pablo Ramos Barroso 7****o 25
Hanna Mendes Levitin h****n@g****m 19
Mike Lin m****n@m****t 10
Venkat Malladi v****i@m****m 5
Aaron Lin 0****l@g****m 3
biocyberman b****n@g****m 3
Christopher Tomkins-Tinch t****c@z****g 2
Christopher Tomkins-Tinch t****c@p****g 2
llangit-broad l****t@b****g 2
cmloreth 6****h 2
Flavia Negrete n****e@w****g 1
Christopher Tomkins-Tinch t****c@h****g 1
Brett T. Hannigan b****n@d****m 1
Katrin Leinweber 9****r 1
pvanheus p****h@w****a 1
Committer Domains (Top 20 + Academic)
broadinstitute.org: 4 webbedfeet.co.za: 1 dnanexus.com: 1 hw-uger-1000.broadinstitute.org: 1 wm1f4-dfc.broadinstitute.org: 1 platinum.broadinstitute.org: 1 ztest2001.broadinstitute.org: 1 microsoft.com: 1 mlin.net: 1 mit.edu: 1 alum.mit.edu: 1 yesimon.com: 1 csail.mit.edu: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 19
  • Total pull requests: 123
  • Average time to close issues: 3 months
  • Average time to close pull requests: 3 days
  • Total issue authors: 2
  • Total pull request authors: 5
  • Average comments per issue: 0.53
  • Average comments per pull request: 0.29
  • Merged pull requests: 112
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 3
  • Pull requests: 39
  • Average time to close issues: 1 day
  • Average time to close pull requests: 10 days
  • Issue authors: 2
  • Pull request authors: 3
  • Average comments per issue: 0.67
  • Average comments per pull request: 0.05
  • Merged pull requests: 30
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • dpark01 (22)
  • tomkinsc (4)
  • marnieya (1)
Pull Request Authors
  • dpark01 (94)
  • tomkinsc (70)
  • jpramosbarroso (6)
  • lakras (5)
  • yesimon (1)
  • mlin (1)
  • golu099 (1)
Top Labels
Issue Labels
bug (1) enhancement (1)
Pull Request Labels

Dependencies

docs/requirements.txt pypi
  • PyYAML *
  • Sphinx *
  • mock *
  • recommonmark *
  • sphinx-argparse *
  • sphinx_rtd_theme *
  • wdl-aid *
requirements-modules.txt pypi
  • andersenlabapps *
  • broadinstitute *
  • nextstrain *
  • quay.io *
.github/workflows/build.yml actions
  • actions/checkout v2 composite
  • actions/setup-java v2 composite
  • actions/setup-python v2 composite
  • docker/setup-buildx-action v1 composite