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pluto-cwl

CWL workflows for helix filter scripts

predector

Effector prediction pipeline based on protein properties.

providencepipeline

quertermous

rna-seq-pipeline

rna_workflow_master

RNA Pipeline for processing mixed RNA/Mouse samples

roswellpark

scrnaseq

A single-cell RNAseq pipeline for 10X genomics data

skylab

Soon to be deprecated in favor of broadinstitute/warp github repo. Previously: Secondary analysis pipelines

snakemake-wrappers

This is the development home of the Snakemake wrapper repository, see

spice-pipeline-cwl

Framework for allele specific analysis of matched tumor and normal next generation sequencing data (CWL version)

stjude_wdl

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

test-datasets

Test data to be used for automated testing with the nf-core pipelines

test_data

topmed-workflows

a place for topmed workflows

umcunextflowmodules

UMCU Genetics Nextflow modules

variant-filtration-cwl

Workflows for filtering GDC VCFs

variantbenchmarking

vep-cwl

GDC VEP Variant Annotation Workflow

viral-ngs-staging

CI staging area between github.com/broadinstitute/viral-pipelines and Dockstore (via Travis)

viral-pipelines

viral-ngs: complete pipelines

virtus

A bioinformatics pipeline for viral transcriptome detection and quantification considering splicing.

warp

WDL Analysis Research Pipelines

wholegenomegermlinesinglesample

wustl

Open workflow definitions for genomic analysis from MGI at WUSM.