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: about 2 months ago - Pushed at: about 2 months ago - Stars: 69 - Forks: 27

Duke-GCB/calrissian

CWL on Kubernetes

Language: Python - Size: 1010 KB - Last synced at: 28 days ago - Pushed at: 6 months ago - Stars: 47 - Forks: 17

stjudecloud/workflows

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

Language: WDL - Size: 74.9 MB - Last synced at: 4 days ago - Pushed at: 5 days ago - Stars: 36 - Forks: 12

ncbi/pm4ngs

Project Manager for NGS data analysis

Language: Python - Size: 14 MB - Last synced at: 30 days ago - Pushed at: almost 3 years ago - Stars: 30 - Forks: 10

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: 3 days ago - Pushed at: over 6 years ago - Stars: 30 - Forks: 5

ncbi/cwl-ngs-workflows-cbb

A set of CWL tools and workflows used by NCBI Computational Biology Branch for NGS data analysis

Language: Common Workflow Language - Size: 629 KB - Last synced at: about 1 year ago - Pushed at: almost 2 years ago - Stars: 24 - Forks: 10

EBI-Metagenomics/pipeline-v5

This repository contains all CWL descriptions of the MGnify pipeline version 5.0.

Language: HTML - Size: 376 MB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 21 - Forks: 20

pughlab/crescent-frontend

CReSCENT: CanceR Single Cell ExpressioN Toolkit | Portal: https://crescent.cloud | Docs: https://pughlab.github.io/crescent-frontend/

Language: R - Size: 124 MB - Last synced at: 6 months ago - Pushed at: about 3 years ago - Stars: 7 - Forks: 2

EBI-Metagenomics/workflow-is-cwl

This repository contains CWL descriptions of the various tools which will allow you to build workflows for the annotation of transcripts

Language: HTML - Size: 30.6 MB - Last synced at: about 1 year ago - Pushed at: about 5 years ago - Stars: 6 - Forks: 7

eliza-m/CrossSpeciesWorkflow

CWL workflow that facilitate performing a series of structural and phenotype related third party prediction methods starting from either a protein FASTA file or a list of Uniprot IDs. Integrated prediction methods refer to secondary structure, solvent accessibility, disordered regions, PTS modifications (phosphorylation, glycosylation, lipid modification, sumoylation, etc).

Language: Python - Size: 6.13 MB - Last synced at: 3 months ago - Pushed at: almost 5 years ago - Stars: 5 - Forks: 3

NCBI-Hackathons/ContainerInception

Gerber: Generalized Easy Reproducible Bioinformatics Environment wRapper

Language: Python - Size: 176 MB - Last synced at: about 1 year ago - Pushed at: about 7 years ago - Stars: 5 - Forks: 4

yonesora56/plant2human

Analysis workflow for novel gene search based on structural similarity search

Language: Jupyter Notebook - Size: 44.1 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 4 - Forks: 0

ICGC-TCGA-PanCancer/pcawg-snv-indel-annotation

This workflow performs annotation on SNV and INDEL VCFs.

Language: JavaScript - Size: 127 KB - Last synced at: 3 months ago - Pushed at: over 7 years ago - Stars: 4 - Forks: 0

Barski-lab/ga4gh_challenge

Workflow for GA4GH/DREAM challenge (phase 2)

Language: Common Workflow Language - Size: 1.63 MB - Last synced at: 3 months ago - Pushed at: about 5 years ago - Stars: 3 - Forks: 5

CBSB/VarCall_CWL

A CWL implementation of a modular GATK Variant Calling pipeline

Language: Shell - Size: 99.6 KB - Last synced at: over 2 years ago - Pushed at: about 6 years ago - Stars: 3 - Forks: 0

msk-access/cwl_subworkflows

A list of subworkflows used for MSK-ACCESS data processing.

Language: Common Workflow Language - Size: 942 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 2 - Forks: 1

rworkflow/RcwlRecipes

Language: Common Workflow Language - Size: 667 KB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 2 - Forks: 3

ForomePlatform/airflow-cwl-docker

Infrastructure as a code for reproducible data science pipelines using CWL and Airflow

Language: Shell - Size: 1.82 MB - Last synced at: over 2 years ago - Pushed at: about 3 years ago - Stars: 2 - Forks: 0

stjudecloud/rfcs

Request for Comments (RFCs) on the St. Jude Cloud Project.

Language: Jupyter Notebook - Size: 4.73 MB - Last synced at: about 2 months ago - Pushed at: 5 months ago - Stars: 1 - Forks: 2

Giulia-Calia/PLANTOGEN-A

PLANTOGEN-A, an automated genome assembly pipeline designed to assemble symbiont microorganisms genome from Oxford Nanopore (ONT) data.

Language: Common Workflow Language - Size: 47.9 KB - Last synced at: over 1 year ago - Pushed at: almost 2 years ago - Stars: 1 - Forks: 0

msk-access/access_qc_generation

Generation Quality Controls Files for MSK-ACCESS

Language: Common Workflow Language - Size: 6.16 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 1

suzuki-shm/GRiD-in-cwl

Growth Rate Index Calculater wrapped by CWL

Language: Common Workflow Language - Size: 4.54 MB - Last synced at: about 1 year ago - Pushed at: over 5 years ago - Stars: 1 - Forks: 0

ICGC-TCGA-PanCancer/pcawg-minibam

Language: JavaScript - Size: 146 KB - Last synced at: 3 months ago - Pushed at: over 6 years ago - Stars: 1 - Forks: 2

eoap/ogc-api-processes-with-zoo

OGC API Processes with ZOO Project

Language: Jupyter Notebook - Size: 3.38 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 0 - Forks: 2

msk-access/uncollapsed_bam_generation

Workflow for making MSK-ACCESS standard binary alignment mapping file.

Language: Common Workflow Language - Size: 1.83 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 2

msk-access/bam_collapsing

Workflow for collapsing of standard binary alignment mapping file generated by MSK-ACCESS

Language: Common Workflow Language - Size: 1.63 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 1

jcaperella29/BWA_SAMTOOLS_CWL_FLOW

a common language workflow , workflow to process Fastq files

Language: Common Workflow Language - Size: 9.77 KB - Last synced at: 3 months ago - Pushed at: 7 months ago - Stars: 0 - Forks: 0

Terradue/ogc-eo-application-package-hands-on

OGC EO Application Package Hands-on

Language: Jupyter Notebook - Size: 757 KB - Last synced at: 3 months ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

cwl-for-eo/otb

CWL examples with the OrfeoToolbox

Language: Common Workflow Language - Size: 23.4 KB - Last synced at: 3 months ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

GusEllerm/GIS_IndexGen

Prototype implementation of LivePaper with GIS indices as the subject.

Language: TypeScript - Size: 92.9 MB - Last synced at: 7 days ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 0

stevekm/toil-elk

Template for running Toil on LSF HPC with ELK stack logging

Language: Makefile - Size: 22.5 KB - Last synced at: 3 months ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

cwl-for-eo/gdal

CWL examples using GDAL

Size: 1.95 KB - Last synced at: over 1 year ago - Pushed at: almost 4 years ago - Stars: 0 - Forks: 0

snap-contrib/example-cwl-sar-calibration-python

Python project example for Sentinel-1 calibration using CWL for the build/test development phase

Language: Python - Size: 13.7 KB - Last synced at: over 1 year ago - Pushed at: almost 4 years ago - Stars: 0 - Forks: 0

suzuki-shm/RaGOO-in-cwl

Wrapper tool of RaGOO by CWL and Docker

Language: Common Workflow Language - Size: 8.79 KB - Last synced at: about 1 year ago - Pushed at: almost 6 years ago - Stars: 0 - Forks: 0

ICGC-TCGA-PanCancer/pcawg-oxog-filter

The CWL workflow to execute the OxoG filter.

Language: Python - Size: 30.3 KB - Last synced at: 3 months ago - Pushed at: over 7 years ago - Stars: 0 - Forks: 0