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atacseq

ATAC-seq peak-calling, QC and differential analysis pipeline

bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis

biocondastats

compile bioconda usage statistics

bixtools

bunny

Reproducible Analyses for Bioinformatics - Java

common-workflow-language

Repository for the CWL standards. Use https://www.biostars.org/t/cwl/ for support 😊

composer

Visual and code editor for Common Workflow Language

cwl-svg

A library for generating an interactive SVG visualization of CWL workflows

cwl-ts

Typescript data model for Common Workflow Language

cwl-v1.1

In development version of the future CWL v1.1 specification

cwl-v1.2

Current development CWL v1.2 specification

cwltool

Common Workflow Language reference implementation

gatk4-somatic-with-preprocessing

gdc-dnaseq-cwl

CWL for GDC DNASeq workflows

image_registry_test

import-cwl-to-sevenbridges

Import CWL to SevenBridges

kf-alignment-workflow

kf-workflows

Bioinformatics workflows for Kids First DRC

rnaseq

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

sbg_dockstore_tools

sevenbridges-python

SevenBridges Python Api bindings

test_bcbio_cwl

Test workflows, run scripts and data for bcbio Common Workflow Language integration

topmed-workflows

a place for topmed workflows

whaaaaat

Inquirer.js port to Python (https://www.npmjs.com/package/inquirer). people blame me for staling this project. I do not have time to work on this right now - whaaaaat do you want me to do? take it offline?