openwdl/wdl

Workflow Description Language - Specification and Implementations

Size: 4.84 MB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 732 - Forks: 301

rnacentre/WDL_dev_10X_DropSeq_SeqWell_BD

WDL workflow language program, developed for singlecell rna sequencing data analysis, maintained by @SunHao(OOAAHH)

Language: WDL - Size: 64.5 KB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 1 - Forks: 0

OOAAHH/SRA_Analysis_WDL

用于bioos的大规模数据分析

Language: WDL - Size: 243 KB - Last synced: 11 days ago - Pushed: 13 days ago - Stars: 1 - Forks: 0

EI-CoreBioinformatics/reat

Robust Eukaryotic Annotation Toolkit

Language: Python - Size: 33.9 MB - Last synced: 8 days ago - Pushed: 4 months ago - Stars: 13 - Forks: 3

stjudecloud/workflows

Bioinformatics workflows developed for and used on the St. Jude Cloud project.

Language: WDL - Size: 9.76 MB - Last synced: 12 days ago - Pushed: 13 days ago - Stars: 30 - Forks: 9

stjudecloud/wdldoc

Create WDL documentation using Markdown.

Language: Python - Size: 360 KB - Last synced: 20 days ago - Pushed: 20 days ago - Stars: 27 - Forks: 5

YogiOnBioinformatics/AALS-Epigenomics-Signal-Reproducibility

Determining reproducibility of Epigenomic signal for Answer ALS

Language: Jupyter Notebook - Size: 46.7 MB - Last synced: 24 days ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

microbiomedata/nmdc-edge

Web-based interface to the NMDC EDGE platform

Language: JavaScript - Size: 326 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 1 - Forks: 0

LUMC/pytest-workflow

Configure workflow/pipeline tests using yaml files.

Language: Python - Size: 756 KB - Last synced: 28 days ago - Pushed: about 2 months ago - Stars: 63 - Forks: 8

broadinstitute/wdl-ide

Rich IDE support for Workflow Description Language

Language: Python - Size: 540 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 39 - Forks: 8

lmtani/pumbaa

Command-line interface for Cromwell server

Language: Go - Size: 8.76 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 16 - Forks: 3

broadinstitute/cromshell

CLI for interacting with Cromwell servers

Language: Python - Size: 684 KB - Last synced: 23 days ago - Pushed: about 2 months ago - Stars: 52 - Forks: 14

XboxDev/Gentoox-Loader 📦

Reconstructed archive of Gentoox-Loader (Cromwell fork)

Language: C - Size: 14.6 MB - Last synced: 2 months ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

stjudecloud/oliver 📦

An opinionated Cromwell orchestration manager.

Language: Python - Size: 2.61 MB - Last synced: about 1 month ago - Pushed: about 1 year ago - Stars: 40 - Forks: 3

XboxDev/cromwell

A free, legal BIOS replacement for the original Xbox

Language: C - Size: 14.6 MB - Last synced: 2 months ago - Pushed: over 1 year ago - Stars: 72 - Forks: 17

antonkulaga/cromwell-client

Client for the Cromwell workflow engine

Language: Scala - Size: 978 KB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 17 - Forks: 4

yjcyxky/choppy-pipe

An integrated analysis platform for efficiently achieving computational reproducibility

Language: Python - Size: 63.8 MB - Last synced: 25 days ago - Pushed: over 1 year ago - Stars: 8 - Forks: 0

FredHutch/diy-cromwell-server

A repo containing instructions for running a Cromwell server on Gizmo at the Fred Hutch. (Contact Amy Paguirigan for questions)

Language: Shell - Size: 156 KB - Last synced: about 1 month ago - Pushed: 3 months ago - Stars: 4 - Forks: 2

broadinstitute/widdler

A command-line tool for executing, managing, and querying WDL workflows on Cromwell servers.

Language: Python - Size: 86.8 MB - Last synced: 7 months ago - Pushed: almost 6 years ago - Stars: 12 - Forks: 6

wsi-hgi-tre/pipelines

Workflow pipelines for the Solita TRE

Language: wdl - Size: 32.2 KB - Last synced: 9 months ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

wtsi-hgi/olly-maersk

Containerisation-agnostic LSF execution configuration for Cromwell

Language: Shell - Size: 72.3 KB - Last synced: about 1 month ago - Pushed: about 5 years ago - Stars: 1 - Forks: 0

wleepang/cromwell-hackathon

utilities for cromwell hackathon

Language: Dockerfile - Size: 5.86 KB - Last synced: 10 months ago - Pushed: about 5 years ago - Stars: 1 - Forks: 0

benben-miao/OmicsFlowBuilder

Omics Flow Builders, such as Cromwell (Java), Nextflow (Java), Snakemake (Python).

Language: Python - Size: 55.7 KB - Last synced: 4 months ago - Pushed: over 1 year ago - Stars: 2 - Forks: 1

yunhailuo/cromwell-authNboard

Dashboard for better visual at workflows on Cromwell server

Language: Python - Size: 13.1 MB - Last synced: 8 months ago - Pushed: over 1 year ago - Stars: 2 - Forks: 0

oicr-gsi/varscan

varscan repo contains code for Varscan workflow

Language: WDL - Size: 164 KB - Last synced: about 1 month ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

labbcb/methseq 📦

Automation tool for high-throughput sequencing DNA methylation data

Language: wdl - Size: 60.5 KB - Last synced: 10 days ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

seandavi/wdlRunR 📦

Elastic, reproducible, and reusable genomic data science tools from R backed by cloud resources

Language: R - Size: 241 KB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 34 - Forks: 7

sgsfak/cwl-progress-cgi

A CGI for getting the status of a workflow execution in Cromwell

Language: C - Size: 483 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

jlboat/Cromwell_PBSPro

An example implementation for the Cromwell workflow management system on PBS Pro

Language: wdl - Size: 22.5 KB - Last synced: 10 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

hisplan/cromwell-gwf-setup

Setting up Cromwell + AWS GWF (Genomics Workflows)

Language: Shell - Size: 8.08 MB - Last synced: about 1 year ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

FaithGriffin/CandidaPhylo

Focused on constructing a phylogenetic tree from Philippine strains of Candida albicans.

Language: wdl - Size: 102 KB - Last synced: about 1 year ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

berguner/atacseq_pipeline

BSF ATAC-seq pipeline

Language: Python - Size: 176 KB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 2 - Forks: 0

hisplan/cromwell-gwf-log

Language: Python - Size: 19.5 KB - Last synced: about 1 year ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

hisplan/wdl-boilerplate

Cromwell+WDL Boilerplate

Language: Shell - Size: 21.5 KB - Last synced: about 1 year ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

TNTurnerLab/ACES

ACES is a workflow to query small sequences in a large set of genomes. It provides several outputs including BLAST results, a multiple sequence alignment file, a graphical fragment assembly file, and a phylogenetic tree file.

Language: Python - Size: 5.67 MB - Last synced: 4 months ago - Pushed: 8 months ago - Stars: 5 - Forks: 0

hisplan/cromsfer

Cromwell Output Transfer

Language: Python - Size: 160 KB - Last synced: about 1 year ago - Pushed: about 2 years ago - Stars: 0 - Forks: 1

labbcb/espresso-caller

Automated and reproducible tool for identifying genomic variants at scale ☕️

Language: wdl - Size: 176 KB - Last synced: 5 days ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

nolwarre/WDL-CI-actions

Example Repository for setting up GitHub Actions for WDL and CWL workflows for CI/CD

Language: wdl - Size: 37.1 KB - Last synced: about 1 year ago - Pushed: about 3 years ago - Stars: 0 - Forks: 1

HaoKuo/NGS-pipeline

GATK and VARSCAN analysis pipeline

Language: Python - Size: 18.6 KB - Last synced: about 1 year ago - Pushed: over 7 years ago - Stars: 1 - Forks: 0

ktaletsk/cwl-examples

Language: Common Workflow Language - Size: 6.84 KB - Last synced: about 1 month ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 0

wtsi-hgi/cromwell-pipelines

Cromwell pipelines for human genetic data

Language: wdl - Size: 62.5 KB - Last synced: about 1 month ago - Pushed: about 5 years ago - Stars: 0 - Forks: 1