A curated list of Nextflow pipelines inspired by other awesome-* lists.
- 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.
- JaneliaSciComp/nextflow-spark
- 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.
- loosolab/TOuCAN - 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.
- tburk/smallRNA-meth - Analyzes smallRNA methylation data.
- 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 also).
- 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 Apache Parquet 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.
- vtilloy/aspicov - 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.
- AveraSD/nextflow-kallisto
- AveraSD/nextflow-rnastar
- cbcrg/benchfam
- cbcrg/grape-nf - Yet another RNA-Seq pipeline (deprecated)
- cerebis/meta-sweeper - Parametric sweep of simulated microbial communities and metagenomic sequencing.
- charite/ngspipeline
- 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.
- fredericlemoine/rna-pipeline
- 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.
- HadrienG/pipelines
- hmkim/workflow
- holtgrewe/ngs_pipelines - Nextflow-based pipelines for typical NGS processing tasks.
- IARCbioinfo/bam_realignment-nf
- IARCbioinfo/bametrics-nf - Compute average metrics from reads that overlap a given set of positions.
- IARCbioinfo/GVCF_pipeline-nf
- IARCbioinfo/mpileup-nf - Coverage computation with samtools mpileup.
- IARCbioinfo/mutect-nf
- InSilicoDB/pipeline-kallisto
- InSilicoDB/snp-imputation-nf
- 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.
- meissnert/nextflow-gtool
- 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
- nmdp-bioinformatics/flow-blast-hml
- nmdp-bioinformatics/flow-validation
- ODiogoSilva/innuca-nf - A nextflow implementation of INNUENDO quality control of reads, de novo assembly and contigs quality assessment.
- pbelmann/sra-download
- 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/nextflow-mapping
- 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
- skner/iasi-pipe
- snewhouse/ngs_nextflow - Alignment, Variant Calling, GATK Best Practices.
- wittelab/orchid - Novel management, annotation, and machine learning framework for analyzing cancer mutations.
- Nextflow training portal by Seqera
- Bioinformatics pipeline example from the bottom up
- CRG course
- Introduction to Bioinformatics workflows with Nextflow and nf-core
- Nextflow patterns - A collection of common Nextflow implementation patterns
- Nextflow tutorial
- Nextflow demos - Example Nextflow pipelines and programming techniques (by Stephen Kelly)
- H3ABioNet course
- Running nf-core pipelines with AWS Batch
- Running nextflow on AWS Batch
- How to make a bigger custom AMI?
- Nextflow on AWS Batch
- Pipelines on AWS
- Reproducible, scalable, and shareable analysis workflows with Nextflow
- Running Nextflow on Google Cloud
- Using AWS Batch to process 67,000 genomes with Bactopia
- Nextflow Beginners Workshop
- nf-core Pre-Hackathon Training 2025
- nextflow-training - by Aubin THOMAS IGH Montpellier
- IARC-nf - List of IARC bioinformatics nextflow pipelines.
- nf-core - 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
- rsuchecki.github.io - Reproducible and Reusable publication and analysis workflow by bioinforad
- CIC Show-and-Tell - Nice Nextflow presentation by @robsyme
- Hello Nextflow training series
- Nextflow: Scalable, Shareable & Reproducible workflows - Awesome intro by Rad Suchecki
- Nextflow Youtube channel
- Using NextFlow pipelines at Babraham
- Nextflow Hackathon '17 - Projects repositorty of the Nextflow Hackathon held in Barcelona, Sept 2017
- Nextflow Workbench - 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.
- NGS workflow Excellent blog post comparing Make/Snakemake/Nextflow by Julian Mazzitelli