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aliquot-maf-cwl

CWL tools and workflows for generating and processing aliquot-MAF

andrewlangvt_wdl

arvados-mrsa

Arvados sequence uploader and analyzer for MRSA project

atac-seq-pipeline

ENCODE ATAC-seq pipeline

bestguess

classify groups based on input

bio-cwl-tools

CWL CommandLineTool descriptions for biology/life-sciences related applications

biocondastats

compile bioconda usage statistics

biowdl-bammetrics

biowdl-input-converter

Converts sample configuration files into WDL structs in JSON format.

biowdl-rna-seq

A BioWDL pipeline for processing RNA-seq data, starting with FASTQ files to produce expression measures and VCFs. Category:Multi-Sample

biowdl-somatic-fastq

biowdl_tasks

A collection of reusable WDL tasks. Category:Other

bisulfite-seq-tools

Suite of tools to conduct methylation data analysis. Methods from this workspace can be used for alignment and quality control analysis for various protocols including Whole Genom Bisulfite Sequencing (WGBS), Reduced Representation Bisulfite Sequencing (RRBS) and Hybrid Selection Bisulfite Sequencing (HSBS).

capanno

cwl/wdl/sm/nf files, tool and workflow metadata, and input specifications.

capanno-utils

Tools to manage repositories of bioinformatics metadata and workflow language files.

chop-dgd-wdl

WDL tasks for commonly used BFX tools

cmrg-benchmarkset-manuscript

Code used to generate manuscript figures and results.

cwl-assembly

cwl-ngs-workflows-cbb

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

d3b-research-workflows

deeppepper

deepvariant-wdl

WDL workflow for population variant calling using htsget, DeepVariant, and GLnexus

dnase-seq-pipeline

ENCODE DNase-seq pipeline

duke

CWL tools and workflows for GGR

ebi-elixir

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

ebi-metagenomics-cwl

This repository contains the CWL description of the EBI Metagenomics pipeline

fda_scrna-seq

fredhutch

Reproducible Workflows, curated at the Fred Hutch

fyrworkshop

gatk-sv