GitHub topics: wdl-workflow
stjude-rust-labs/sprocket-vscode
Visual Studio Code extension for Sprocket (https://github.com/stjude-rust-labs/sprocket).
Language: TypeScript - Size: 627 KB - Last synced at: 36 minutes ago - Pushed at: about 2 hours ago - Stars: 6 - Forks: 10
stjude-rust-labs/wdl
Rust crates for working with Workflow Description Language (WDL) documents.
Language: Rust - Size: 3.5 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 48 - Forks: 34
stjude-rust-labs/sprocket
A bioinformatics workflow engine built on top of the Workflow Description Language (WDL).
Language: Rust - Size: 743 KB - Last synced at: 2 days ago - Pushed at: 6 days ago - Stars: 68 - Forks: 10
stjude-rust-labs/sprocket-action
Run Sprocket WDL document validation as part of a CI/CD pipeline with GitHub Actions.
Language: Shell - Size: 385 KB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 6 - Forks: 1
stjudecloud/workflows
Bioinformatics workflows developed for and used on the St. Jude Cloud project.
Language: WDL - Size: 74.7 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 36 - Forks: 12
microbiomedata/metaAssembly
Workflow for metagenome assembly
Language: WDL - Size: 11.1 MB - Last synced at: 8 days ago - Pushed at: 27 days ago - Stars: 4 - Forks: 4
4dn-dcic/tibanna
Tibanna helps you run your genomic pipelines on Amazon cloud (AWS). It is used by the 4DN DCIC (4D Nucleome Data Coordination and Integration Center) to process data. Tibanna supports CWL/WDL (w/ docker), Snakemake (w/ conda) and custom Docker/shell command.
Language: Python - Size: 134 MB - Last synced at: 10 days ago - Pushed at: 10 days ago - Stars: 69 - Forks: 27
oicr-gsi/strelkaSomatic
Strelka2 somatic variant calling workflow
Language: WDL - Size: 61.5 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 1 - Forks: 0
getwilds/ww-salmon
Self-contained WDL workflow that uses the Salmon RNA-seq computational tool.
Language: WDL - Size: 21.5 KB - Last synced at: about 1 month ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 0
getwilds/ww-sourmash
Self-contained WDL workflow that uses Sourmash to perform similarity searches between sequence files.
Language: WDL - Size: 11.7 KB - Last synced at: about 1 month ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0
getwilds/ww-shapemapper
Self-contained WDL workflow that uses Shapemapper
Language: WDL - Size: 17.6 KB - Last synced at: about 1 month ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0
getwilds/ww-vc-trio
Variant calling WDL workflow using a trio of variant callers and analyzing consensus among them
Language: WDL - Size: 26.4 KB - Last synced at: about 1 month ago - Pushed at: 10 months ago - Stars: 0 - Forks: 2
stjudecloud/rfcs
Request for Comments (RFCs) on the St. Jude Cloud Project.
Language: Jupyter Notebook - Size: 4.73 MB - Last synced at: 7 days ago - Pushed at: 3 months ago - Stars: 1 - Forks: 2
openwdl/cookbook
Illustrative examples using WDL best practices.
Size: 104 KB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 0 - Forks: 0
stjudecloud/wdldoc
Create WDL documentation using Markdown.
Language: Python - Size: 157 KB - Last synced at: 8 days ago - Pushed at: 14 days ago - Stars: 27 - Forks: 5
chopdgd/bfx-tools-wdl
WDL tasks for commonly used BFX tools
Language: WDL - Size: 348 KB - Last synced at: 28 days ago - Pushed at: 2 months ago - Stars: 5 - Forks: 5
getwilds/ww-demo-workflows Fork of FredHutch/wdl-test-workflows
A repo containing workflows written in WDL to test using the Fred Hutch Cromwell configuration.
Language: WDL - Size: 2.55 MB - Last synced at: 7 days ago - Pushed at: 4 months ago - Stars: 1 - Forks: 0
rnacentre/WDL_Tools
WDL workflow language program, developed for singlecell rna sequencing data analysis, maintained by @OOAAHH(SunHao) .
Language: WDL - Size: 78.5 MB - Last synced at: about 1 month ago - Pushed at: 4 months ago - Stars: 2 - Forks: 1
getwilds/ww-star-deseq2
Relatively straightforward WDL workflow that executes STAR+DESeq2 on RNAseq data
Language: WDL - Size: 2.68 MB - Last synced at: about 1 month ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0
getwilds/ww-sra-star
Workflow to download paired fastqs from SRA and pass through STAR 2 pass
Language: WDL - Size: 29.3 KB - Last synced at: about 1 month ago - Pushed at: 10 months ago - Stars: 0 - Forks: 0
getwilds/ww-cell-ranger
A basic starting point for a cell ranger workflow
Language: WDL - Size: 22.5 KB - Last synced at: about 1 month ago - Pushed at: 10 months ago - Stars: 0 - Forks: 0
getwilds/ww-fastq-to-cram
Self-contained WDL workflow that converts a WGS FASTQ file into an unmapped CRAM file
Language: WDL - Size: 2.54 MB - Last synced at: about 1 month ago - Pushed at: 10 months ago - Stars: 0 - Forks: 0
fhdsl/AnVIL_Data_Subsetting
Tutorial for running the fastq_subsample WDL workflow on AnVIL!
Language: CSS - Size: 14.6 MB - Last synced at: about 2 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0
broadinstitute/fungal-wdl
Broad fungal method repository
Language: WDL - Size: 95.7 KB - Last synced at: 9 months ago - Pushed at: over 1 year ago - Stars: 6 - Forks: 4
getwilds/wdl-101
This is the repository for the WDL and JSON files accompanying the WDL 101 course.
Language: WDL - Size: 55.7 KB - Last synced at: 7 days ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0
stjudecloud/oliver 📦
An opinionated Cromwell orchestration manager.
Language: Python - Size: 2.61 MB - Last synced at: 12 months ago - Pushed at: about 2 years ago - Stars: 40 - Forks: 3
anand-imcm/pb-variant-call
Variant Calling and Annotation using PacBio Hi-Fi Reads
Language: WDL - Size: 59.6 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0
broadinstitute/widdler
A command-line tool for executing, managing, and querying WDL workflows on Cromwell servers.
Language: Python - Size: 86.8 MB - Last synced at: 9 months ago - Pushed at: over 6 years ago - Stars: 13 - Forks: 6
CCBR/HERVx
Pipeline to characterize Human Endogenous Retrovirus (HERV) expression
Language: Shell - Size: 5.75 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 3 - Forks: 3
MobiDL/tasks
A collection of tasks wrapped in WDL
Language: wdl - Size: 695 KB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 1 - Forks: 1
common-workflow-lab/wdl2cwl 📦
[Experimental] Workflow Definition Language (WDL) to CWL
Language: Python - Size: 179 KB - Last synced at: 29 days ago - Pushed at: over 3 years ago - Stars: 28 - Forks: 4
Sentieon/Sentieon-WDL
WDL pipelines for the Sentieon tools
Language: wdl - Size: 33.2 KB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 4 - Forks: 2
otiai10/hotsub
Command line tool to run batch jobs concurrently with ETL framework on AWS or other cloud computing resources
Language: Go - Size: 283 KB - Last synced at: 6 days ago - Pushed at: over 6 years ago - Stars: 30 - Forks: 5
weinstockj/telomere-length-pipeline
A cloud-based pipeline to estimate telomere lengths from WGS data using Telseq
Language: wdl - Size: 8.79 KB - Last synced at: about 2 months ago - Pushed at: about 6 years ago - Stars: 3 - Forks: 1
lvn3668/ArgoWorkflowGenerator
Java based workflow generator to deploy WES variant detection pipelines on Kubernetes using Argo. Reads WDL files and produces Argo compatible work flows specifciying compute cluster environment (pod) on which the workflow component should be executed and the buckets in which the results should be dropped
Language: Java - Size: 493 KB - Last synced at: about 1 year ago - Pushed at: almost 4 years ago - Stars: 1 - Forks: 0
alexmondaini/RNA_seq-EPRINT
RNA binding workflow geared towards broad discovery of binding sites
Language: wdl - Size: 43.9 KB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 0
jvandinter/MitoCallPipeline
A pipeline for mitochondrial mutation calling
Language: HTML - Size: 18.2 MB - Last synced at: almost 2 years ago - Pushed at: almost 5 years ago - Stars: 3 - Forks: 0
biowdl/sequence-classification
A workflow for processing metagenomics data sets using Centrifuge. Category:Single-Sample
Language: wdl - Size: 6.78 MB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 1
FaithGriffin/CandidaPhylo
Focused on constructing a phylogenetic tree from Philippine strains of Candida albicans.
Language: wdl - Size: 102 KB - Last synced at: almost 2 years ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 0
ga4gh-tech-team/wdl-hello-world
Workflow Description Language (WDL) test workflow. Write hardcoded messages to stdout. For testing Cloud WS APIs and the GA4GH Starter Kit.
Language: wdl - Size: 6.84 KB - Last synced at: about 2 years ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 0
ga4gh-tech-team/wdl-echo
Workflow Description Language (WDL) test workflow. Write custom messages as file outputs. For testing Cloud WS APIs and the GA4GH Starter Kit.
Language: wdl - Size: 5.86 KB - Last synced at: about 2 years ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 0