vsmalladi

ampliseq

16S rRNA amplicon sequencing analysis workflow using QIIME2

atac-seq-pipeline

ENCODE ATAC-seq pipeline

autouri

Recursive localization for various types of URIs

configs

Config files used to define parameters specific to compute environments at different Institutions

cromwell

Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments

CromwellOnAzure

Microsoft Genomics supported implementation of the Broad Institute's Cromwell workflow engine on Azure

ga4gh-starter-kit-wes

Starter Kit server implementation of the GA4GH Workflow Execution Service (WES) specification

hlatyping

Precision HLA typing from next-generation sequencing data

images

mag

Assembly and binning of metagenomes

modules

Repository to host tool-specific module files for the Nextflow DSL2 community!

MultiQC

Aggregate results from bioinformatics analyses across many samples into a single report.

MultiQC_TestData

Test data for MultiQC. See https://github.com/ewels/MultiQC

nanoseq

Nanopore demultiplexing, QC and alignment pipeline

nf-core-testnf

nf-core-tower-azure-poc

nf-sentieon

POC Nextflow pipeline to run Sentieon software

pb-human-wgs-workflow-snakemake

Workflow for the comprehensive detection and prioritization of variants in human genomes with PacBio HiFi reads

pb-human-wgs-workflow-wdl

public_health_viral_genomics

Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of viral pathogens of concern, especially SARS-CoV-2

RNA-seq

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

rnaseq-nf

A proof of concept of RNAseq pipeline

sarek

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

task-execution-schemas

test-docker

tools

Python package with helper tools for the nf-core community.

viral-pipelines

viral-ngs: complete pipelines

warp

WDL Analysis Research Pipelines

wdl101

workflow-execution-service-schemas

The WES API is a standard way to run and manage portable workflows.