awesome-nextflow

cbcrg/ampa-nf

Automated prediction of protein antimicrobial regions

cbcrg/mta-nf

A method for best alignment of evaluation trees

nextflow-io/rnaseq-nf

A basic pipeline for quantification of RNA-seq data using Salmon

nextflow-io/rnatoy

A basic RNA-seq pipeline

nextflow-io/elixir-workshop-21

A basic pipeline with QC and alignment

AndersenLab/cegwas2-nf

GWA mapping with C. elegans

alesssia/YAMP

Yet Another Metagenomic Pipeline

anvlasova/FA-nf

Functional annotation pipeline for proteins from non-model organisms

biocorecrg/allele_specific_RNAseq

Allele-specific RNA-seq pipeline

bactopia/bactopia

A flexible pipeline for complete analysis of bacterial genomes

biocorecrg/ExOrthist

ExOrthist is a Nextflow based pipeline to infer exon orthology groups at all evolutionary distances

biocorecrg/indrop

Single cell transcriptome analysis pipeline based on DropEst

biocorecrg/master_of_pores

Nextflow pipeline for analysis of Nanopore reads

biocorecrg/MOP2

DSL2 version of master of pores. Faster and better

biocorecrg/transcriptome_assembly

De novo transcriptome assembly and annotations workflow based on trinity / transdecoder

biocorecrg/vectorQC

A Nextflow pipeline for assembling and annotating vectors

brwnj/smoove-nf

Smoove workflow for Structural Variant calling and Quality Control

cbcrg/kallisto-nf

Nextflow implementation of Kallisto & Sleuth RNA-Seq Tools

cbcrg/piper-nf

RNA mapping pipeline

cbcrg/unistrap

Reliability measure of inferred phylogenetic trees

crickbabs/BABS-aDNASeq

An ancient DNA nextflow analysis pipeline

CRG-CNAG/CalliNGS-NF

Variant Calling Analysis with RNA-Seq data based on GATK best practices

Dowell-Lab/ChIP-Flow

Nextflow pipeline for ChIP-seq analysis

Dowell-Lab/RNAseq-Flow

Nextflow pipeline for processing RNA-seq data

Dowell-Lab/Nascent-Flow

Nascent Transcription Processing Pipeline

FredHutch/reproducible-workflows

Reproducible Workflows, curated at the Fred Hutch

guigolab/chip-nf

Automated ChIP-seq pipeline

guigolab/grape-nf

Automated RNA-seq pipeline

guigolab/ipsa-nf

Integrative Pipeline for Splicing Analyses

guigolab/FA-nf

Functional annotation pipeline for proteins from non-model organisms

h3abionet/h3abionet16S

Integrated pipeline for 16S rDNA diversity analysis

IARC/needlestack

Multi-sample somatic variant caller

IARC/gatk4-GenotypeGVCFs-nf

Joint calling of gVCF, following GATK4 Best Practices

IARC/gatk4-HaplotypeCaller-nf

GATK4 HaplotypeCaller step, in gVCF mode, first step for subsequent whole cohort Joint Genotyping

icgc-argo/sanger-wgs-variant-calling

Sanger WGS Variant Caller

jdidion/atropos

NGS read trimming tool that is specific, sensitive, and speedy

labsyspharm/mcmicro

End-to-end pipeline for processing multiplexed whole slide imaging and tissue microarrays

Targeted chrOmatin Capture ANalysis

metagenomics/MeRaGENE

Metagenomics rapid gene identification pipeline

mirnylab/distiller-nf

Modular Hi-C mapping pipeline

montilab/pipeliner

Framework for the definition of sequencing data processing workflows

NCBI-Hackathons/ATACFlow

ATAC-seq pipeline wrapped in NextFlow

NCSA/GenomicsCortextVarNextflow

Structural Variant Calling with Cortex-Var

nf-core/chipseq

Chromatin immunoprecipitation (ChIP-seq) peak-calling, QC and differential analysis pipeline

nf-core/eager

A fully reproducible and state of the art ancient DNA analysis pipeline

nf-core/hlatyping

Precision HLA typing from next-generation sequencing data

nf-core/lncpipe

Analysis of long non-coding RNAs from RNA-seq datasets

nf-core/mag

Assembly and binning of metagenomes

nf-core/methylseq

Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel

nf-core/pangenome

Renders a collection of sequences into a pangenome graph

nf-core/rnaseq

RNA sequencing analysis pipeline using STAR, HISAT2 and Salmon with gene counts and quality control

nf-core/rnafusion

RNA sequencing analysis pipeline with curated list of tools for detecting and visualizing fusion genes

nf-core/sarek

Analysis pipeline to detect germline or somatic variants from WGS / targeted sequencing

nf-core/smrnaseq

A small-RNA sequencing analysis pipeline

nf-core/vipr

Assembly and intrahost / low-frequency variant calling for viral samples

nf-core/viralrecon

Assembly and intrahost/low-frequency variant calling for viral samples

nmdp-bioinformatics/flow

Consensus assembly and variant calling workflow

robsyme/nf-repeatmasking

Workflow for automatic repeat detection, classification and masking

qbicsoftware/icgc-featurecounts

Pipeline to run featureCounts on RNAseq BAM files

sanger-pathogens/companion

Eukaryotic genome annotation pipeline

ZuberLab/crispr-process-nf

Process CRISPR and shRNA functional genetic screening data

ZuberLab/mageck-nf

Statistical Analysis of multiplexed CRISPR / shRNA Screens using MAGeCK

biocorecrg/master_of_pores

Nextflow pipeline for analysis of Nanopore data from direct RNA sequencing (see )

BU-ISCIII/SARS-Cov2_analysis

SARS-Cov2 bioinformatics analysis

connor-lab/ncov2019-artic-nf

A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools with a focus on ncov2019

heuermh/sars-cov-2

Transform SARS-CoV-2 annotated genomes into sequences and features in format

jnoms/virID

Viral Identification and Discovery - A viral characterization pipeline built in Nextflow

nf-core/viralrecon

Assembly and intrahost/low-frequency variant calling for viral samples

Automated and Standardized Pipeline for Identification of SARS-Cov2 nucleotidic Variants

abreschi/ShortRNA-nf

Pipeline for processing shortRNA-seq data

andremrsantos/next-pipes-lghm

Eukaryotic genome annotation pipeline

cbcrg/grape-nf

Yet another RNA-Seq pipeline (deprecated)

cerebis/meta-sweeper

Parametric sweep of simulated microbial communities and metagenomic sequencing

chrisquince/DESMAN

De novo Extraction of Strains from MetAgeNomes

evanfloden/concTree

Creates consensus trees using alignment uncertainty from many MSAs

evanfloden/lncRNA-Annotation-nf

lncRNA Annotation Pipeline based on STAR, Cufflinks and FEELnc

evanfloden/paraMSA

Multiple sequence alignments for phylogenetic trees and bootstrap support values

evanfloden/tuxedo-nf

Nextflow implementation of the Tuxedo Suite of Tools

evanfloden/vast-tools-nf

Nextflow Implementation of VAST-TOOLS for profiling alternative splicing events in RNA-Seq data

h3abionet/chipimputation

Imputation workflow developed as part of the H3 Africa BioNet Hackathon

h3abionet/h3agwas

GWAS pipeline developed as part of the H3 Africa BioNet Hackathon

holtgrewe/ngs_pipelines

Nextflow-based pipelines for typical NGS processing tasks

IARCbioinfo/bametrics-nf

Compute average metrics from reads that overlap a given set of positions

IARCbioinfo/mpileup-nf

Coverage computation with samtools mpileup

jdidion/rna-quick

Rapid analysis of gene and transcript quantification and differential expression

joshua-d-campbell/nf-GATK_Exome_Preprocess

GATK best practice guide to preprocess whole exome sequencing (WES) data

CDCgov/mycosnp-nf

Portable workflow for performing whole genome sequencing analysis of fungal organisms

NationalGenomicsInfrastructure/icing

HLA typing from OxfordNanopore reads

NBISweden/wgs-structvar

Genome Sequenceing Structural Variation Pipelines

MHH-RCUG/nf_wochenende

A metagenomic (and genomic) alignment and normalization pipeline for long and short reads

ODiogoSilva/innuca-nf

A nextflow implementation of INNUENDO quality control of reads, de novo assembly and contigs quality assessment

CDCgov/PHoeNIx

A short-read pipeline for healthcare-associated and antimicrobial resistant pathogens

PlantandFoodResearch/VariantAnalysis

Bioinformatic variant calling pipeline

robsyme/nextflow-annotate

Fungal genome annotation workflow

robsyme/workflows-proteogenomics

Versioned, shareable and replicable workflows for proteogenomics

CDCgov/SC2CLIA

Pipeline for Clinical Laboratories Improvements Amendments (CLIA) compliant variant calling and spike protein substitution prediction with additional tools for quality control

Alignment, Variant Calling, GATK Best Practices

wittelab/orchid

Novel management, annotation, and machine learning framework for analyzing cancer mutations

Nextflow patterns

A collection of common Nextflow implementation patterns

Nextflow demos

Example Nextflow pipelines and programming techniques (by Stephen Kelly)

IARC-nf

List of bioinformatics nextflow pipelines

A collection of high quality Nextflow pipelines

biocorecrg/BioNextflow

Repository to host DSL2 based tool-specific sub-workflows

nf-core/modules

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

UMCUGenetics/NextflowModules

UMCU Genetics Nextflow modules

Reproducible and Reusable publication and analysis workflow by

Nice Nextflow presentation by

Awesome intro by Rad Suchecki

Nextflow Hackathon '17

Projects repositorty of the Nextflow Hackathon held in Barcelona, Sept 2017

Workbench that make it easier to write data analysis workflows with Nextflow

nf-core/tools

Helper tools for the nf-core community, linting, template

Make to Nextflow

Converts Makefile to Nextflow

NCBI-Hackathons/SPeW

A discussion comparting different workflow frameworks including Nextflow

Excellent blog post comparing Make/Snakemake/Nextflow by Julian Mazzitelli