awesome-nextflow

Biological workflows

A curated collection of reusable workflow pipelines for various biological analysis tasks.

A curated list of nextflow based pipelines

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last commit: about 3 years ago
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Awesome Nextflow / Example pipelines
cbcrg/ampa-nf 5 over 3 years ago Automated prediction of protein antimicrobial regions
cbcrg/mta-nf 2 over 7 years ago A method for best alignment of evaluation trees
nextflow-io/rnaseq-nf 74 about 1 year ago A basic pipeline for quantification of RNA-seq data using Salmon
nextflow-io/rnatoy 33 almost 5 years ago A basic RNA-seq pipeline
nextflow-io/elixir-workshop-21 5 almost 4 years ago A basic pipeline with QC and alignment
AndersenLab/cegwas2-nf 8 over 1 year ago GWA mapping with C. elegans
alesssia/YAMP 57 over 2 years ago Yet Another Metagenomic Pipeline
anvlasova/FA-nf 3 about 7 years ago Functional annotation pipeline for proteins from non-model organisms
biocorecrg/allele_specific_RNAseq 10 11 months ago Allele-specific RNA-seq pipeline
bactopia/bactopia 423 12 months ago A flexible pipeline for complete analysis of bacterial genomes
biocorecrg/ExOrthist 21 11 months ago ExOrthist is a Nextflow based pipeline to infer exon orthology groups at all evolutionary distances
biocorecrg/indrop 6 almost 6 years ago Single cell transcriptome analysis pipeline based on DropEst
biocorecrg/master_of_pores 95 11 months ago Nextflow pipeline for analysis of Nanopore reads
biocorecrg/MOP2 23 11 months ago DSL2 version of master of pores. Faster and better
biocorecrg/transcriptome_assembly 3 about 2 years ago De novo transcriptome assembly and annotations workflow based on trinity / transdecoder
biocorecrg/vectorQC 5 about 4 years ago A Nextflow pipeline for assembling and annotating vectors
brwnj/smoove-nf 12 almost 5 years ago Smoove workflow for Structural Variant calling and Quality Control
cbcrg/kallisto-nf 22 over 7 years ago Nextflow implementation of Kallisto & Sleuth RNA-Seq Tools
cbcrg/piper-nf 18 over 7 years ago RNA mapping pipeline
cbcrg/unistrap 6 over 7 years ago Reliability measure of inferred phylogenetic trees
crickbabs/BABS-aDNASeq 2 about 7 years ago An ancient DNA nextflow analysis pipeline
CRG-CNAG/CalliNGS-NF 132 almost 3 years ago Variant Calling Analysis with RNA-Seq data based on GATK best practices
Dowell-Lab/ChIP-Flow 4 over 2 years ago Nextflow pipeline for ChIP-seq analysis
Dowell-Lab/RNAseq-Flow 8 over 2 years ago Nextflow pipeline for processing RNA-seq data
Dowell-Lab/Nascent-Flow 8 almost 2 years ago Nascent Transcription Processing Pipeline
FredHutch/reproducible-workflows 12 over 6 years ago Reproducible Workflows, curated at the Fred Hutch
guigolab/chip-nf 17 about 3 years ago Automated ChIP-seq pipeline
guigolab/grape-nf 37 about 1 year ago Automated RNA-seq pipeline
guigolab/ipsa-nf 9 over 6 years ago Integrative Pipeline for Splicing Analyses
guigolab/FA-nf 17 over 3 years ago Functional annotation pipeline for proteins from non-model organisms
h3abionet/h3abionet16S 18 over 6 years ago Integrated pipeline for 16S rDNA diversity analysis
JaneliaSciComp/nextflow-spark 14 about 3 years ago
IARC/needlestack 50 almost 4 years ago Multi-sample somatic variant caller
IARC/gatk4-GenotypeGVCFs-nf 12 over 6 years ago Joint calling of gVCF, following GATK4 Best Practices
IARC/gatk4-HaplotypeCaller-nf 8 almost 6 years ago GATK4 HaplotypeCaller step, in gVCF mode, first step for subsequent whole cohort Joint Genotyping
icgc-argo/sanger-wgs-variant-calling 0 about 4 years ago Sanger WGS Variant Caller
jdidion/atropos 120 almost 2 years ago NGS read trimming tool that is specific, sensitive, and speedy
labsyspharm/mcmicro 115 11 months ago End-to-end pipeline for processing multiplexed whole slide imaging and tissue microarrays
loosolab/TOuCAN Targeted chrOmatin Capture ANalysis
metagenomics/MeRaGENE 4 about 7 years ago Metagenomics rapid gene identification pipeline
mirnylab/distiller-nf 87 11 months ago Modular Hi-C mapping pipeline
montilab/pipeliner 44 about 6 years ago Framework for the definition of sequencing data processing workflows
NCBI-Hackathons/ATACFlow 14 almost 7 years ago ATAC-seq pipeline wrapped in NextFlow
NCSA/GenomicsCortextVarNextflow 2 over 6 years ago Structural Variant Calling with Cortex-Var
nf-core/chipseq 199 11 months ago Chromatin immunoprecipitation (ChIP-seq) peak-calling, QC and differential analysis pipeline
nf-core/eager 152 11 months ago A fully reproducible and state of the art ancient DNA analysis pipeline
nf-core/hlatyping 63 11 months ago Precision HLA typing from next-generation sequencing data
nf-core/lncpipe 34 over 1 year ago Analysis of long non-coding RNAs from RNA-seq datasets
nf-core/mag 219 11 months ago Assembly and binning of metagenomes
nf-core/methylseq 148 11 months ago Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
nf-core/pangenome 78 11 months ago Renders a collection of sequences into a pangenome graph
nf-core/rnaseq 941 11 months ago RNA sequencing analysis pipeline using STAR, HISAT2 and Salmon with gene counts and quality control
nf-core/rnafusion 147 11 months ago RNA sequencing analysis pipeline with curated list of tools for detecting and visualizing fusion genes
nf-core/sarek 412 11 months ago Analysis pipeline to detect germline or somatic variants from WGS / targeted sequencing
nf-core/smrnaseq 74 11 months ago A small-RNA sequencing analysis pipeline
nf-core/vipr 14 over 5 years ago Assembly and intrahost / low-frequency variant calling for viral samples
nf-core/viralrecon 128 11 months ago Assembly and intrahost/low-frequency variant calling for viral samples
nmdp-bioinformatics/flow 12 over 10 years ago Consensus assembly and variant calling workflow
robsyme/nf-repeatmasking 13 over 7 years ago Workflow for automatic repeat detection, classification and masking
qbicsoftware/icgc-featurecounts 3 about 7 years ago Pipeline to run featureCounts on RNAseq BAM files
sanger-pathogens/companion 21 over 4 years ago Eukaryotic genome annotation pipeline
tburk/smallRNA-meth
ZuberLab/crispr-process-nf 3 about 1 year ago Process CRISPR and shRNA functional genetic screening data
ZuberLab/mageck-nf 3 over 7 years ago Statistical Analysis of multiplexed CRISPR / shRNA Screens using MAGeCK
biocorecrg/master_of_pores 95 11 months ago Nextflow pipeline for analysis of Nanopore data from direct RNA sequencing (see )
BU-ISCIII/SARS-Cov2_analysis 11 over 5 years ago SARS-Cov2 bioinformatics analysis
connor-lab/ncov2019-artic-nf 91 about 2 years ago A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools with a focus on ncov2019
heuermh/sars-cov-2 1 about 4 years ago Transform SARS-CoV-2 annotated genomes into sequences and features in format
jnoms/virID 11 over 5 years ago Viral Identification and Discovery - A viral characterization pipeline built in Nextflow
nf-core/viralrecon 128 11 months 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 8 years ago Pipeline for processing shortRNA-seq data
andremrsantos/next-pipes-lghm 3 over 10 years ago Eukaryotic genome annotation pipeline
AveraSD/nextflow-kallisto 3 over 10 years ago
AveraSD/nextflow-rnastar 4 over 10 years ago
cbcrg/benchfam 3 almost 8 years ago
cbcrg/grape-nf 2 over 7 years ago Yet another RNA-Seq pipeline (deprecated)
cerebis/meta-sweeper 10 over 3 years ago Parametric sweep of simulated microbial communities and metagenomic sequencing
charite/ngspipeline 7 almost 11 years ago
chrisquince/DESMAN 69 over 5 years ago De novo Extraction of Strains from MetAgeNomes
evanfloden/concTree 6 over 7 years ago Creates consensus trees using alignment uncertainty from many MSAs
evanfloden/lncRNA-Annotation-nf 11 over 7 years ago lncRNA Annotation Pipeline based on STAR, Cufflinks and FEELnc
evanfloden/paraMSA 4 over 7 years ago Multiple sequence alignments for phylogenetic trees and bootstrap support values
evanfloden/tuxedo-nf 10 over 7 years ago Nextflow implementation of the Tuxedo Suite of Tools
evanfloden/vast-tools-nf 5 over 7 years ago Nextflow Implementation of VAST-TOOLS for profiling alternative splicing events in RNA-Seq data
fredericlemoine/rna-pipeline 4 over 6 years ago
h3abionet/chipimputation 20 about 1 year ago Imputation workflow developed as part of the H3 Africa BioNet Hackathon
h3abionet/h3agwas 108 11 months ago GWAS pipeline developed as part of the H3 Africa BioNet Hackathon
HadrienG/pipelines 2 almost 9 years ago
hmkim/workflow 9 almost 7 years ago
holtgrewe/ngs_pipelines 6 over 10 years ago Nextflow-based pipelines for typical NGS processing tasks
IARCbioinfo/bam_realignment-nf 1 over 9 years ago
IARCbioinfo/bametrics-nf 1 over 8 years ago Compute average metrics from reads that overlap a given set of positions
IARCbioinfo/GVCF_pipeline-nf 4 almost 9 years ago
IARCbioinfo/mpileup-nf 1 almost 8 years ago Coverage computation with samtools mpileup
IARCbioinfo/mutect-nf 9 over 1 year ago
InSilicoDB/pipeline-kallisto 3 almost 10 years ago
InSilicoDB/snp-imputation-nf 1 over 9 years ago
jdidion/rna-quick 4 over 5 years ago Rapid analysis of gene and transcript quantification and differential expression
joshua-d-campbell/nf-GATK_Exome_Preprocess 10 about 6 years ago GATK best practice guide to preprocess whole exome sequencing (WES) data
meissnert/nextflow-gtool 2 over 10 years ago
CDCgov/mycosnp-nf 38 11 months ago Portable workflow for performing whole genome sequencing analysis of fungal organisms
NationalGenomicsInfrastructure/icing 13 about 7 years ago HLA typing from OxfordNanopore reads
NBISweden/wgs-structvar 16 over 6 years ago Genome Sequenceing Structural Variation Pipelines
MHH-RCUG/nf_wochenende 13 11 months ago A metagenomic (and genomic) alignment and normalization pipeline for long and short reads
nmdp-bioinformatics/flow-blast-hml 1 over 9 years ago
nmdp-bioinformatics/flow-validation 2 over 10 years ago
ODiogoSilva/innuca-nf 3 almost 8 years ago A nextflow implementation of INNUENDO quality control of reads, de novo assembly and contigs quality assessment
pbelmann/sra-download 6 over 6 years ago
CDCgov/PHoeNIx 60 11 months ago A short-read pipeline for healthcare-associated and antimicrobial resistant pathogens
PlantandFoodResearch/VariantAnalysis 5 about 9 years ago Bioinformatic variant calling pipeline
robsyme/nextflow-annotate 20 over 2 years ago Fungal genome annotation workflow
robsyme/nextflow-mapping
robsyme/workflows-proteogenomics 2 almost 11 years ago Versioned, shareable and replicable workflows for proteogenomics
CDCgov/SC2CLIA 4 almost 4 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 10 years ago
snewhouse/ngs_nextflow Alignment, Variant Calling, GATK Best Practices
wittelab/orchid 31 over 1 year 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 8 years ago
Introduction to Bioinformatics workflows with Nextflow and nf-core
Nextflow patterns 336 almost 2 years ago A collection of common Nextflow implementation patterns
Nextflow tutorial 32 over 7 years ago
Nextflow training by Seqera Labs
Nextflow demos 103 11 months ago Example Nextflow pipelines and programming techniques (by Stephen Kelly)
H3ABioNet course 6 over 2 years 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 48 over 1 year ago List of bioinformatics nextflow pipelines
nf-core A collection of high quality Nextflow pipelines

Awesome Nextflow / Modules collections
biocorecrg/BioNextflow 26 11 months ago Repository to host DSL2 based tool-specific sub-workflows
nf-core/modules 287 11 months ago Repository to host tool-specific module files for the Nextflow DSL2 community
UMCUGenetics/NextflowModules 27 about 1 year 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 about 1 year ago
Sublime Text 24 almost 3 years ago
VIM 48 over 2 years ago
VSCode 32 11 months ago
Nextflow Hackathon '17 10 about 8 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 245 11 months ago Helper tools for the nf-core community, linting, template
Make to Nextflow 5 about 6 years ago Converts Makefile to Nextflow
NCBI-Hackathons/SPeW 26 about 8 years ago A discussion comparting different workflow frameworks including Nextflow
NGS workflow Excellent blog post comparing Make/Snakemake/Nextflow by Julian Mazzitelli

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