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/rnatoy - A basic RNA-seq pipeline
- nextflow-io/rnaseq-nf - A basic pipeline for quantification of RNA-seq data using Salmon.
- alesssia/YAMP - Yet Another Metagenomic Pipeline.
- cbcrg/piper-nf - RNA mapping pipeline.
- cbcrg/kallisto-nf - Nextflow implementation of Kallisto & Sleuth RNA-Seq Tools.
- cbcrg/unistrap - Reliability measure of inferred phylogenetic trees.
- CRG-CNAG/CalliNGS-NF - Variant Calling Analysis with RNA-Seq data based on GATK best practices.
- iarcbioinfo/needlestack - Multi-sample somatic variant caller.
- guigolab/chip-nf - Automated ChIP-seq pipeline.
- guigolab/grape-nf - Automated RNA-seq pipeline.
- guigolab/ipsa-nf - Integrative Pipeline for Splicing Analyses.
- h3abionet/h3abionet16S - Integrated pipeline for 16S rDNA diversity analysis.
- jdidion/atropos - NGS read trimming tool that is specific, sensitive, and speedy.
- likelet/LncPipe - A Nextflow-based pipeline for lncRNA discovery and comprehensive analysis from un processed RNA-seq data.
- metagenomics/MeRaGENE - Metagenomics rapid gene identification pipeline.
- mirnylab/distiller-nf - Modular Hi-C mapping pipeline.
- mfoll/robust-regression-caller - Robust regression multi-sample variant caller.
- montilab/pipeliner - Framework for the definition of sequencing data processing workflows.
- nmdp-bioinformatics/flow - Consensus assembly and variant calling workflow.
- robsyme/nf-repeatmasking - Workflow for automatic repeat detection, classification and masking.
- sanger-pathogens/companion - Eukaryotic genome annotation pipeline.
- SciLifeLab/Sarek - Detect germline or somatic variants from normal or tumour/normal WGS.
- SciLifeLab/NGI-ExoSeq - Exome Sequencing Best Practice analysis pipeline.
- SciLifeLab/NGI-RNAseq - SciLifeLab NGI RNA-seq analysis pipeline.
- SciLifeLab/NGI-smRNAseq - SciLifeLab NGI small RNA-seq analysis pipeline.
- SciLifeLab/NGI-MethylSeq - SciLifeLab NGI Methylation (Bisulfite-Seq) analysis pipeline.
- SciLifeLab/NGI-ChIPseq - SciLifeLab NGI RNA-seq ChIP-seq analysis pipeline.
- skptic/concTree - Creates consensus trees using alignment uncertainty from many MSAs.
- skptic/lncRNA-Annotation-nf - lncRNA Annotation Pipeline based on STAR, Cufflinks and FEELnc.
- skptic/paraMSA - Multiple sequence alignments for phylogenetic trees and bootstrap support values.
- skptic/vast-tools-nf - Nextflow Implementation of VAST-TOOLS for profiling alternative splicing events in RNA-Seq data.
- skptic/tuxedo-nf - Nextflow implementation of the Tuxedo Suite of Tools.
- tburk/smallRNA-meth - Analyzes smallRNA methylation data.
- ZuberLab/mageck-nf - Statistical Analysis of multiplexed CRISPR / shRNA Screens using MAGeCK.
- abreschi/ShortRNA-nf - Pipeline for processing shortRNA-seq data.
- andremrsantos/next-pipes-lghm - Eukaryotic genome annotation pipeline.
- averasd/nextflow-kallisto
- averasd/nextflow-rnastar
- bihealth/ngs_pipelines
- 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.
- ODiogoSilva/innuca-nf - A nextflow implementation of INNUENDO quality control of reads, de novo assembly and contigs quality assessment.
- 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
- heuermh/bdg-nextflow - Transform BAM files found recursively in a given directory to ADAM format.
- 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.
- JWCarlson/interflowscan - Implements the protein analysis components of InterProScan5 using Nextflow.
- pbelmann/sra-download
- phelelani/filtering-pipeline - Assembly pipeline for exogenous reads filtered from human RNA-seq data.
- 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.
- meissnert/nextflow-gtool
- NationalGenomicsInfrastructure/icing - HLA typing from OxfordNanopore reads.
- NBISweden/wgs-structvar - Genome Sequenceing Structural Variation Pipelines.
- nmdp-bioinformatics/flow-validation
- nmdp-bioinformatics/flow-blast-hml
- 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.
- CRG course
- Nextflow demos - Example Nextflow pipelines and programming techniques (by Stephen Kelly)
- Nextflow tutorial
- H3ABioNet course
- IARC-nf - List of IARC bioinformatics nextflow pipelines.
- NF-Core - A collection of high quality Nextflow pipelines.
- CIC Show-and-Tell - Nice Nextflow presentation by @robsyme
- Nextflow Hackathon '17 - Projects repositorty of the Nextflow Hackathon held in Barcelona, Sept 2017
- Nextflow Toys - Scripts for efficiently dealing with Nextflow
- Nextflow Workbench - Workbench that make it easier to write data analysis workflows with Nextflow
- NF-Core/Cookiecutter - Template for your own top-end Nextflow pipeline, customised using Cookiecutter.
- 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