awesome-nextflow
Biological workflows
A curated collection of reusable workflow pipelines for various biological analysis tasks.
A curated list of nextflow based pipelines
572 stars
33 watching
90 forks
last commit: about 2 years ago
Linked from 1 awesome list
awesome-listnextflow
Awesome Nextflow / Example pipelines | |||
| cbcrg/ampa-nf | 5 | over 2 years ago | Automated prediction of protein antimicrobial regions |
| cbcrg/mta-nf | 2 | over 6 years ago | A method for best alignment of evaluation trees |
| nextflow-io/rnaseq-nf | 72 | 15 days ago | A basic pipeline for quantification of RNA-seq data using Salmon |
| nextflow-io/rnatoy | 33 | almost 4 years ago | A basic RNA-seq pipeline |
| nextflow-io/elixir-workshop-21 | 5 | almost 3 years ago | A basic pipeline with QC and alignment |
Awesome Nextflow / Featured pipelines | |||
| AndersenLab/cegwas2-nf | 8 | 6 months ago | GWA mapping with C. elegans |
| alesssia/YAMP | 56 | over 1 year ago | Yet Another Metagenomic Pipeline |
| anvlasova/FA-nf | 3 | about 6 years ago | Functional annotation pipeline for proteins from non-model organisms |
| biocorecrg/allele_specific_RNAseq | 9 | 7 months ago | Allele-specific RNA-seq pipeline |
| bactopia/bactopia | 413 | 10 days ago | A flexible pipeline for complete analysis of bacterial genomes |
| biocorecrg/ExOrthist | 21 | 18 days ago | ExOrthist is a Nextflow based pipeline to infer exon orthology groups at all evolutionary distances |
| biocorecrg/indrop | 6 | almost 5 years ago | Single cell transcriptome analysis pipeline based on DropEst |
| biocorecrg/master_of_pores | 93 | about 2 months ago | Nextflow pipeline for analysis of Nanopore reads |
| biocorecrg/MOP2 | 23 | about 1 year ago | DSL2 version of master of pores. Faster and better |
| biocorecrg/transcriptome_assembly | 3 | about 1 year ago | De novo transcriptome assembly and annotations workflow based on trinity / transdecoder |
| biocorecrg/vectorQC | 5 | over 3 years ago | A Nextflow pipeline for assembling and annotating vectors |
| brwnj/smoove-nf | 12 | about 4 years ago | Smoove workflow for Structural Variant calling and Quality Control |
| cbcrg/kallisto-nf | 22 | over 6 years ago | Nextflow implementation of Kallisto & Sleuth RNA-Seq Tools |
| cbcrg/piper-nf | 18 | over 6 years ago | RNA mapping pipeline |
| cbcrg/unistrap | 6 | over 6 years ago | Reliability measure of inferred phylogenetic trees |
| crickbabs/BABS-aDNASeq | 2 | about 6 years ago | An ancient DNA nextflow analysis pipeline |
| CRG-CNAG/CalliNGS-NF | 132 | almost 2 years ago | Variant Calling Analysis with RNA-Seq data based on GATK best practices |
| Dowell-Lab/ChIP-Flow | 4 | over 1 year ago | Nextflow pipeline for ChIP-seq analysis |
| Dowell-Lab/RNAseq-Flow | 8 | over 1 year ago | Nextflow pipeline for processing RNA-seq data |
| Dowell-Lab/Nascent-Flow | 8 | 10 months ago | Nascent Transcription Processing Pipeline |
| FredHutch/reproducible-workflows | 12 | over 5 years ago | Reproducible Workflows, curated at the Fred Hutch |
| guigolab/chip-nf | 17 | about 2 years ago | Automated ChIP-seq pipeline |
| guigolab/grape-nf | 37 | 2 months ago | Automated RNA-seq pipeline |
| guigolab/ipsa-nf | 9 | over 5 years ago | Integrative Pipeline for Splicing Analyses |
| guigolab/FA-nf | 17 | over 2 years ago | Functional annotation pipeline for proteins from non-model organisms |
| h3abionet/h3abionet16S | 18 | over 5 years ago | Integrated pipeline for 16S rDNA diversity analysis |
| JaneliaSciComp/nextflow-spark | 14 | about 2 years ago | |
| IARC/needlestack | 49 | almost 3 years ago | Multi-sample somatic variant caller |
| IARC/gatk4-GenotypeGVCFs-nf | 11 | over 5 years ago | Joint calling of gVCF, following GATK4 Best Practices |
| IARC/gatk4-HaplotypeCaller-nf | 8 | almost 5 years ago | GATK4 HaplotypeCaller step, in gVCF mode, first step for subsequent whole cohort Joint Genotyping |
| icgc-argo/sanger-wgs-variant-calling | 0 | about 3 years ago | Sanger WGS Variant Caller |
| jdidion/atropos | 120 | 12 months ago | NGS read trimming tool that is specific, sensitive, and speedy |
| labsyspharm/mcmicro | 111 | about 1 month ago | End-to-end pipeline for processing multiplexed whole slide imaging and tissue microarrays |
| loosolab/TOuCAN | Targeted chrOmatin Capture ANalysis | ||
| metagenomics/MeRaGENE | 4 | about 6 years ago | Metagenomics rapid gene identification pipeline |
| mirnylab/distiller-nf | 87 | 12 months ago | Modular Hi-C mapping pipeline |
| montilab/pipeliner | 44 | about 5 years ago | Framework for the definition of sequencing data processing workflows |
| NCBI-Hackathons/ATACFlow | 14 | almost 6 years ago | ATAC-seq pipeline wrapped in NextFlow |
| NCSA/GenomicsCortextVarNextflow | 2 | over 5 years ago | Structural Variant Calling with Cortex-Var |
| nf-core/chipseq | 194 | about 1 month ago | Chromatin immunoprecipitation (ChIP-seq) peak-calling, QC and differential analysis pipeline |
| nf-core/eager | 148 | 9 days ago | A fully reproducible and state of the art ancient DNA analysis pipeline |
| nf-core/hlatyping | 63 | about 1 month ago | Precision HLA typing from next-generation sequencing data |
| nf-core/lncpipe | 33 | 7 months ago | Analysis of long non-coding RNAs from RNA-seq datasets |
| nf-core/mag | 216 | 25 days ago | Assembly and binning of metagenomes |
| nf-core/methylseq | 140 | 9 days ago | Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel |
| nf-core/pangenome | 78 | about 1 month ago | Renders a collection of sequences into a pangenome graph |
| nf-core/rnaseq | 916 | 15 days ago | RNA sequencing analysis pipeline using STAR, HISAT2 and Salmon with gene counts and quality control |
| nf-core/rnafusion | 143 | 9 days ago | RNA sequencing analysis pipeline with curated list of tools for detecting and visualizing fusion genes |
| nf-core/sarek | 409 | 6 days ago | Analysis pipeline to detect germline or somatic variants from WGS / targeted sequencing |
| nf-core/smrnaseq | 74 | 11 days ago | A small-RNA sequencing analysis pipeline |
| nf-core/vipr | 14 | almost 5 years ago | Assembly and intrahost / low-frequency variant calling for viral samples |
| nf-core/viralrecon | 124 | 16 days ago | Assembly and intrahost/low-frequency variant calling for viral samples |
| nmdp-bioinformatics/flow | 12 | over 9 years ago | Consensus assembly and variant calling workflow |
| robsyme/nf-repeatmasking | 13 | almost 7 years ago | Workflow for automatic repeat detection, classification and masking |
| qbicsoftware/icgc-featurecounts | 3 | over 6 years ago | Pipeline to run featureCounts on RNAseq BAM files |
| sanger-pathogens/companion | 21 | over 3 years ago | Eukaryotic genome annotation pipeline |
| tburk/smallRNA-meth | |||
| ZuberLab/crispr-process-nf | 3 | about 1 month ago | Process CRISPR and shRNA functional genetic screening data |
| ZuberLab/mageck-nf | 3 | over 6 years ago | Statistical Analysis of multiplexed CRISPR / shRNA Screens using MAGeCK |
Awesome Nextflow / Covid-19 related projects | |||
| biocorecrg/master_of_pores | 93 | about 2 months ago | Nextflow pipeline for analysis of Nanopore data from direct RNA sequencing (see ) |
| BU-ISCIII/SARS-Cov2_analysis | 11 | over 4 years ago | SARS-Cov2 bioinformatics analysis |
| connor-lab/ncov2019-artic-nf | 89 | about 1 year ago | A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools with a focus on ncov2019 |
| heuermh/sars-cov-2 | 1 | about 3 years ago | Transform SARS-CoV-2 annotated genomes into sequences and features in format |
| jnoms/virID | 11 | over 4 years ago | Viral Identification and Discovery - A viral characterization pipeline built in Nextflow |
| nf-core/viralrecon | 124 | 16 days ago | Assembly and intrahost/low-frequency variant calling for viral samples |
| vtilloy/aspicov | Automated and Standardized Pipeline for Identification of SARS-Cov2 nucleotidic Variants | ||
Awesome Nextflow / Other pipelines | |||
| abreschi/ShortRNA-nf | 3 | over 7 years ago | Pipeline for processing shortRNA-seq data |
| andremrsantos/next-pipes-lghm | 3 | over 9 years ago | Eukaryotic genome annotation pipeline |
| AveraSD/nextflow-kallisto | 3 | over 9 years ago | |
| AveraSD/nextflow-rnastar | 4 | over 9 years ago | |
| cbcrg/benchfam | 3 | almost 7 years ago | |
| cbcrg/grape-nf | 2 | over 6 years ago | Yet another RNA-Seq pipeline (deprecated) |
| cerebis/meta-sweeper | 10 | over 2 years ago | Parametric sweep of simulated microbial communities and metagenomic sequencing |
| charite/ngspipeline | 7 | almost 10 years ago | |
| chrisquince/DESMAN | 69 | over 4 years ago | De novo Extraction of Strains from MetAgeNomes |
| evanfloden/concTree | 6 | over 6 years ago | Creates consensus trees using alignment uncertainty from many MSAs |
| evanfloden/lncRNA-Annotation-nf | 11 | over 6 years ago | lncRNA Annotation Pipeline based on STAR, Cufflinks and FEELnc |
| evanfloden/paraMSA | 4 | over 6 years ago | Multiple sequence alignments for phylogenetic trees and bootstrap support values |
| evanfloden/tuxedo-nf | 10 | over 6 years ago | Nextflow implementation of the Tuxedo Suite of Tools |
| evanfloden/vast-tools-nf | 5 | over 6 years ago | Nextflow Implementation of VAST-TOOLS for profiling alternative splicing events in RNA-Seq data |
| fredericlemoine/rna-pipeline | 4 | over 5 years ago | |
| h3abionet/chipimputation | 20 | 18 days ago | Imputation workflow developed as part of the H3 Africa BioNet Hackathon |
| h3abionet/h3agwas | 106 | 2 months ago | GWAS pipeline developed as part of the H3 Africa BioNet Hackathon |
| HadrienG/pipelines | 2 | almost 8 years ago | |
| hmkim/workflow | 9 | almost 6 years ago | |
| holtgrewe/ngs_pipelines | 6 | over 9 years ago | Nextflow-based pipelines for typical NGS processing tasks |
| IARCbioinfo/bam_realignment-nf | 1 | over 8 years ago | |
| IARCbioinfo/bametrics-nf | 1 | over 7 years ago | Compute average metrics from reads that overlap a given set of positions |
| IARCbioinfo/GVCF_pipeline-nf | 4 | about 8 years ago | |
| IARCbioinfo/mpileup-nf | 1 | almost 7 years ago | Coverage computation with samtools mpileup |
| IARCbioinfo/mutect-nf | 9 | 7 months ago | |
| InSilicoDB/pipeline-kallisto | 3 | almost 9 years ago | |
| InSilicoDB/snp-imputation-nf | 1 | over 8 years ago | |
| jdidion/rna-quick | 4 | over 4 years ago | Rapid analysis of gene and transcript quantification and differential expression |
| joshua-d-campbell/nf-GATK_Exome_Preprocess | 10 | about 5 years ago | GATK best practice guide to preprocess whole exome sequencing (WES) data |
| meissnert/nextflow-gtool | 2 | over 9 years ago | |
| CDCgov/mycosnp-nf | 37 | 2 months ago | Portable workflow for performing whole genome sequencing analysis of fungal organisms |
| NationalGenomicsInfrastructure/icing | 13 | over 6 years ago | HLA typing from OxfordNanopore reads |
| NBISweden/wgs-structvar | 15 | over 5 years ago | Genome Sequenceing Structural Variation Pipelines |
| MHH-RCUG/nf_wochenende | 13 | about 1 month ago | A metagenomic (and genomic) alignment and normalization pipeline for long and short reads |
| nmdp-bioinformatics/flow-blast-hml | 1 | over 8 years ago | |
| nmdp-bioinformatics/flow-validation | 2 | over 9 years ago | |
| ODiogoSilva/innuca-nf | 3 | almost 7 years ago | A nextflow implementation of INNUENDO quality control of reads, de novo assembly and contigs quality assessment |
| pbelmann/sra-download | 6 | over 5 years ago | |
| CDCgov/PHoeNIx | 59 | 8 days ago | A short-read pipeline for healthcare-associated and antimicrobial resistant pathogens |
| PlantandFoodResearch/VariantAnalysis | 5 | about 8 years ago | Bioinformatic variant calling pipeline |
| robsyme/nextflow-annotate | 20 | over 1 year ago | Fungal genome annotation workflow |
| robsyme/nextflow-mapping | |||
| robsyme/workflows-proteogenomics | 2 | almost 10 years ago | Versioned, shareable and replicable workflows for proteogenomics |
| CDCgov/SC2CLIA | 4 | almost 3 years ago | Pipeline for Clinical Laboratories Improvements Amendments (CLIA) compliant variant calling and spike protein substitution prediction with additional tools for quality control |
| skner/iasi-pipe | 2 | over 9 years ago | |
| snewhouse/ngs_nextflow | Alignment, Variant Calling, GATK Best Practices | ||
| wittelab/orchid | 31 | 5 months ago | Novel management, annotation, and machine learning framework for analyzing cancer mutations |
Awesome Nextflow / Tutorials | |||
| Bioinformatics pipeline example from the bottom up | |||
| CRG course | 23 | about 7 years ago | |
| Introduction to Bioinformatics workflows with Nextflow and nf-core | |||
| Nextflow patterns | 334 | about 1 year ago | A collection of common Nextflow implementation patterns |
| Nextflow tutorial | 32 | over 6 years ago | |
| Nextflow training by Seqera Labs | |||
| Nextflow demos | 101 | 3 months ago | Example Nextflow pipelines and programming techniques (by Stephen Kelly) |
| H3ABioNet course | 6 | over 1 year ago | |
| 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 | |||
Awesome Nextflow / Pipelines collections | |||
| IARC-nf | 47 | 4 months ago | List of bioinformatics nextflow pipelines |
| nf-core | A collection of high quality Nextflow pipelines | ||
Awesome Nextflow / Modules collections | |||
| biocorecrg/BioNextflow | 26 | 9 days ago | Repository to host DSL2 based tool-specific sub-workflows |
| nf-core/modules | 283 | 5 days ago | Repository to host tool-specific module files for the Nextflow DSL2 community |
| UMCUGenetics/NextflowModules | 26 | 30 days ago | UMCU Genetics Nextflow modules |
Awesome Nextflow / Presentations | |||
| rsuchecki.github.io | Reproducible and Reusable publication and analysis workflow by | ||
| CIC Show-and-Tell | Nice Nextflow presentation by | ||
Awesome Nextflow / Video | |||
| Nextflow: Scalable, Shareable & Reproducible workflows | Awesome intro by Rad Suchecki | ||
| Nextflow Youtube channel | |||
| Using NextFlow pipelines at Babraham | |||
Awesome Nextflow / Syntax highlighting | |||
| Atom | |||
| Emacs | 20 | 2 months ago | |
| Sublime Text | 24 | almost 2 years ago | |
| VIM | 48 | over 1 year ago | |
| VSCode | 32 | 6 days ago | |
Awesome Nextflow / Other links | |||
| Nextflow Hackathon '17 | 10 | about 7 years ago | 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 | 242 | 5 days ago | Helper tools for the nf-core community, linting, template |
| Make to Nextflow | 5 | about 5 years ago | Converts Makefile to Nextflow |
| NCBI-Hackathons/SPeW | 26 | about 7 years ago | A discussion comparting different workflow frameworks including Nextflow |
| NGS workflow | Excellent blog post comparing Make/Snakemake/Nextflow by Julian Mazzitelli | ||
raivivek/awesome-biology
vpetukhov/ggrastr
cupy/cupy
unslothai/hyperlearn
dena/chainer_mask_r-cnn
cortes-ciriano-lab/scomatic
arogozhnikov/einops
jdidion/biotools