Awesome Nextflow

A curated list of Nextflow pipelines inspired by other awesome-* lists.

Example pipelines

• 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

Featured pipelines

• 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.

Covid-19 related projects

• 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.

Other pipelines

• 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.

Tutorials

• 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 training by Seqera Labs

• 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

Pipelines collections

• IARC-nf - List of IARC bioinformatics nextflow pipelines.

• nf-core - A collection of high quality Nextflow pipelines.

Modules collections

• 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

Presentations

• rsuchecki.github.io - Reproducible and Reusable publication and analysis workflow by bioinforad

• CIC Show-and-Tell - Nice Nextflow presentation by @robsyme

Video

• Nextflow: Scalable, Shareable & Reproducible workflows - Awesome intro by Rad Suchecki

• Nextflow Youtube channel

• Using NextFlow pipelines at Babraham

Syntax highlighting

• Atom

• Emacs

• Sublime Text

• VIM

• VSCode

Other links

• 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