https://github.com/broadinstitute/drop-seq-wdl
Science Score: 36.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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✓Committers with academic emails
1 of 1 committers (100.0%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (7.4%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: broadinstitute
- License: mit
- Language: WDL
- Default Branch: main
- Size: 104 KB
Statistics
- Stars: 0
- Watchers: 3
- Forks: 0
- Open Issues: 4
- Releases: 15
Metadata Files
README.md
Drop-seq WDL
WDL for analyzing Drop-seq data
Drop-seq questions may be directed to dropseq@gmail.com.
You may also use this address to be added to the Drop-seq Google group.
See the Drop-seq GitHub repository for more information on the tools.
Overview
These WDLs are considered early but usable previews, subject to extensive changes!
WDLs are separated by into pipelines and tasks
- Pipelines are the top-level WDLs that define the executable workflows.
- Some pipelines are further divided into sub-workflows.
- Tasks are the individual steps that are called by the pipelines that execute a single tool.
- There are experimental "combined" WDLs that aggregate multiple pipelines.
The WDLs are designed to
- Run on Terra.bio platform and its underlying Cromwell workflow management system.
- Written in WDL version 1.0.
- Optimize costs on Google Cloud Platform but may run on other platforms.
- Compliment and extend pipelines from
- WARP, especially Optimus.
- CellBender Remove Background (CBRB)
- pyQTL
- sc-eQTLs in cell villages pipeline
- broadinstitute_gtex
- Optimize Google Compute memory while leaving a buffer, with Java Virtual Machines sized to use a fraction of the
host VM memory, since as of July 2025
- Terra.bio does not retry any host VM memory failures when triggering the OOM Killer, plus...
- Google Cloud Batch often fails with 50002 errors when the host is under strain as the Batch agent does not seem to reserve compute resources for itself.
Tasks contain a mix of Drop-seq tools and other tools
- Drop-seq tools are from the Drop-seq GitHub repository.
- Other tools are from the Broad Institute GATK and other sources.
- Tasks may expose all or only some of the tool parameters.
Workflows
| Workflow | Summary |
|---------------------------|-------------------------------------------------|
| optimus_post_processing | Converts Optimus outputs to Drop-seq inputs |
| dropseq_cbrb | Estimates parameters then invokes CBRB |
| cell_selection | Sub-selects barcodes that captured nuclei |
| standard_analysis | Assigns nuclei to donors and detects doublets |
| cell_classification | Classifies cells based on their gene expression |
| tensorqtl | cis-QTL mapping using tensorQTL |
Owner
- Name: Broad Institute
- Login: broadinstitute
- Kind: organization
- Location: Cambridge, MA
- Website: http://www.broadinstitute.org/
- Twitter: broadinstitute
- Repositories: 1,083
- Profile: https://github.com/broadinstitute
Broad Institute of MIT and Harvard
GitHub Events
Total
- Create event: 36
- Issues event: 6
- Release event: 14
- Delete event: 22
- Issue comment event: 2
- Push event: 64
- Pull request event: 33
Last Year
- Create event: 36
- Issues event: 6
- Release event: 14
- Delete event: 22
- Issue comment event: 2
- Push event: 64
- Pull request event: 33
Committers
Last synced: about 1 year ago
Top Committers
| Name | Commits | |
|---|---|---|
| kshakir | k****r@b****g | 11 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 4
- Total pull requests: 30
- Average time to close issues: about 1 month
- Average time to close pull requests: about 16 hours
- Total issue authors: 1
- Total pull request authors: 2
- Average comments per issue: 0.0
- Average comments per pull request: 0.0
- Merged pull requests: 25
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 4
- Pull requests: 30
- Average time to close issues: about 1 month
- Average time to close pull requests: about 16 hours
- Issue authors: 1
- Pull request authors: 2
- Average comments per issue: 0.0
- Average comments per pull request: 0.0
- Merged pull requests: 25
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- kshakir (4)
Pull Request Authors
- kshakir (28)
- alecw (1)