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A curated list of nextflow based pipelines
https://github.com/nextflow-io/awesome-nextflow
List: awesome-nextflow
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A curated list of nextflow based pipelines
Host: GitHub
URL: https://github.com/nextflow-io/awesome-nextflow
Owner: nextflow-io
License: cc0-1.0
Created: 2015-07-27T21:58:11.000Z (over 9 years ago)
Default Branch: master
Last Pushed: 2022-10-27T17:15:09.000Z (about 2 years ago)
Last Synced: 2024-07-28T13:05:34.740Z (3 months ago)
Topics: awesome-list, nextflow
Homepage:
Size: 156 KB
Stars: 563
Watchers: 34
Forks: 90
Open Issues: 2
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project

awesome-awesomeness-bioinformatics - Awesome Nextflow
awesome-AI-kubernetes - Awesome Nextflow
README

        Awesome Nextflow

=================

A curated list of Nextflow pipelines inspired by other [awesome-*](https://github.com/bayandin/awesome-awesomeness) lists.

Example pipelines

-------------------

* [cbcrg/ampa-nf](https://github.com/cbcrg/ampa-nf) - Automated prediction of protein antimicrobial regions

* [cbcrg/mta-nf](https://github.com/cbcrg/mta-nf) - A method for best alignment of evaluation trees

* [nextflow-io/rnaseq-nf](https://github.com/nextflow-io/rnaseq-nf) - A basic pipeline for quantification of RNA-seq data using Salmon.

* [nextflow-io/rnatoy](https://github.com/nextflow-io/rnatoy) - A basic RNA-seq pipeline

* [nextflow-io/elixir-workshop-21](https://github.com/nextflow-io/elixir-workshop-21) - A basic pipeline with QC and alignment 

Featured pipelines

-------------------

* [AndersenLab/cegwas2-nf](https://github.com/AndersenLab/cegwas2-nf) - GWA mapping with C. elegans.

* [alesssia/YAMP](https://github.com/alesssia/YAMP) - Yet Another Metagenomic Pipeline.

* [anvlasova/FA-nf](https://github.com/anvlasova/FA-nf) - Functional annotation pipeline for proteins from non-model organisms.

* [biocorecrg/allele_specific_RNAseq](https://github.com/biocorecrg/allele_specific_RNAseq) - Allele-specific RNA-seq pipeline

* [bactopia/bactopia](https://github.com/bactopia/bactopia) - A flexible pipeline for complete analysis of bacterial genomes.

* [biocorecrg/ExOrthist](https://github.com/biocorecrg/ExOrthist) - ExOrthist is a Nextflow based pipeline to infer exon orthology groups at all evolutionary distances.

* [biocorecrg/indrop](https://github.com/biocorecrg/indrop)- Single cell transcriptome analysis pipeline based on DropEst.

* [biocorecrg/master_of_pores](https://github.com/biocorecrg/master_of_pores) -  Nextflow pipeline for analysis of Nanopore reads.

* [biocorecrg/MOP2](https://github.com/biocorecrg/MOP2) -  DSL2 version of master of pores. Faster and better. 

* [biocorecrg/transcriptome_assembly](https://github.com/biocorecrg/transcriptome_assembly) - De novo transcriptome assembly and annotations workflow based on trinity / transdecoder. 

* [biocorecrg/vectorQC](https://github.com/biocorecrg/vectorQC) - A Nextflow pipeline for assembling and annotating vectors. 

* [brwnj/smoove-nf](https://github.com/brwnj/smoove-nf) - Smoove workflow for Structural Variant calling and Quality Control.

* [cbcrg/kallisto-nf](https://github.com/cbcrg/kallisto-nf) - Nextflow implementation of Kallisto & Sleuth RNA-Seq Tools.

* [cbcrg/piper-nf](https://github.com/cbcrg/piper-nf) - RNA mapping pipeline.

* [cbcrg/unistrap](https://github.com/cbcrg/unistrap) - Reliability measure of inferred phylogenetic trees.

* [crickbabs/BABS-aDNASeq](https://github.com/crickbabs/BABS-aDNASeq) - An ancient DNA nextflow analysis pipeline.

* [CRG-CNAG/CalliNGS-NF](https://github.com/CRG-CNAG/CalliNGS-NF) - Variant Calling Analysis with RNA-Seq data based on GATK best practices.

* [Dowell-Lab/ChIP-Flow](https://github.com/Dowell-Lab/ChIP-Flow) - Nextflow pipeline for ChIP-seq analysis.

* [Dowell-Lab/RNAseq-Flow](https://github.com/Dowell-Lab/RNAseq-Flow) - Nextflow pipeline for processing RNA-seq data.

* [Dowell-Lab/Nascent-Flow](https://github.com/Dowell-Lab/Nascent-Flow) - Nascent Transcription Processing Pipeline.

* [FredHutch/reproducible-workflows](https://github.com/FredHutch/reproducible-workflows/tree/master/nextflow) - Reproducible Workflows, curated at the Fred Hutch.

* [guigolab/chip-nf](https://github.com/guigolab/chip-nf) - Automated ChIP-seq pipeline.

* [guigolab/grape-nf](https://github.com/guigolab/grape-nf) - Automated RNA-seq pipeline.

* [guigolab/ipsa-nf](https://github.com/guigolab/ipsa-nf) - Integrative Pipeline for Splicing Analyses.

* [guigolab/FA-nf](https://github.com/guigolab/FA-nf) - Functional annotation pipeline for proteins from non-model organisms 

* [h3abionet/h3abionet16S](https://github.com/h3abionet/h3abionet16S) - Integrated pipeline for 16S rDNA diversity analysis.

* [JaneliaSciComp/nextflow-spark](https://github.com/JaneliaSciComp/nextflow-spark)

* [IARC/needlestack](https://github.com/IARCbioinfo/needlestack) - Multi-sample somatic variant caller.

* [IARC/gatk4-GenotypeGVCFs-nf](https://github.com/IARCbioinfo/gatk4-GenotypeGVCFs-nf) - Joint calling of gVCF, following GATK4 Best Practices.

* [IARC/gatk4-HaplotypeCaller-nf](https://github.com/IARCbioinfo/gatk4-HaplotypeCaller-nf) - GATK4 HaplotypeCaller step, in gVCF mode, first step for subsequent whole cohort Joint Genotyping.

* [icgc-argo/sanger-wgs-variant-calling](https://github.com/icgc-argo/sanger-wgs-variant-calling) - Sanger WGS Variant Caller.

* [jdidion/atropos](https://github.com/jdidion/atropos/tree/main/paper) - NGS read trimming tool that is specific, sensitive, and speedy.

* [labsyspharm/mcmicro](https://github.com/labsyspharm/mcmicro) - End-to-end pipeline for processing multiplexed whole slide imaging and tissue microarrays.

* [loosolab/TOuCAN](https://github.molgen.mpg.de/loosolab/TOuCAN) - Targeted chrOmatin Capture ANalysis.

* [metagenomics/MeRaGENE](https://github.com/metagenomics/MeRaGENE) - Metagenomics rapid gene identification pipeline.

* [mirnylab/distiller-nf](https://github.com/mirnylab/distiller-nf) - Modular Hi-C mapping pipeline.

* [montilab/pipeliner](https://github.com/montilab/pipeliner) - Framework for the definition of sequencing data processing workflows.

* [NCBI-Hackathons/ATACFlow](https://github.com/NCBI-Hackathons/ATACFlow) - ATAC-seq pipeline wrapped in NextFlow.

* [NCSA/GenomicsCortextVarNextflow](https://github.com/ncsa/GenomicsCortextVarNextflow) - Structural Variant Calling with Cortex-Var.

* [nf-core/chipseq](https://github.com/nf-core/chipseq) - Chromatin immunoprecipitation (ChIP-seq) peak-calling, QC and differential analysis pipeline.

* [nf-core/eager](https://github.com/nf-core/eager) - A fully reproducible and state of the art ancient DNA analysis pipeline.

* [nf-core/hlatyping](https://github.com/nf-core/hlatyping) - Precision HLA typing from next-generation sequencing data.

* [nf-core/lncpipe](https://github.com/nf-core/lncpipe) - Analysis of long non-coding RNAs from RNA-seq datasets.

* [nf-core/mag](https://github.com/nf-core/mag) - Assembly and binning of metagenomes.

* [nf-core/methylseq](https://github.com/nf-core/methylseq) - Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel.

* [nf-core/pangenome](https://github.com/nf-core/pangenome) - Renders a collection of sequences into a pangenome graph.

* [nf-core/rnaseq](https://github.com/nf-core/rnaseq) - RNA sequencing analysis pipeline using STAR, HISAT2 and Salmon with gene counts and quality control.

* [nf-core/rnafusion](https://github.com/nf-core/rnafusion) - RNA sequencing analysis pipeline with curated list of tools for detecting and visualizing fusion genes.

* [nf-core/sarek](https://github.com/nf-core/sarek) - Analysis pipeline to detect germline or somatic variants from WGS / targeted sequencing.

* [nf-core/smrnaseq](https://github.com/nf-core/smrnaseq) - A small-RNA sequencing analysis pipeline.

* [nf-core/vipr](https://github.com/nf-core/vipr) - Assembly and intrahost / low-frequency variant calling for viral samples.

* [nf-core/viralrecon](https://github.com/nf-core/viralrecon/) - Assembly and intrahost/low-frequency variant calling for viral samples.

* [nmdp-bioinformatics/flow](https://github.com/nmdp-bioinformatics/flow) - Consensus assembly and variant calling workflow.

* [robsyme/nf-repeatmasking](https://github.com/robsyme/nf-repeatmasking) - Workflow for automatic repeat detection, classification and masking.

* [qbicsoftware/icgc-featurecounts](https://github.com/qbicsoftware/icgc-featurecounts) - Pipeline to run featureCounts on RNAseq BAM files.

* [sanger-pathogens/companion](https://github.com/sanger-pathogens/companion) - Eukaryotic genome annotation pipeline.

* [tburk/smallRNA-meth](https://gitlab.com/tburk/smallRNA-meth) - [Analyzes smallRNA methylation data](https://www.nature.com/articles/nmeth.4610).

* [ZuberLab/crispr-process-nf](https://github.com/ZuberLab/crispr-process-nf) - Process CRISPR and shRNA functional genetic screening data.

* [ZuberLab/mageck-nf](https://github.com/ZuberLab/mageck-nf) - Statistical Analysis of multiplexed CRISPR / shRNA Screens using MAGeCK.

Covid-19 related projects

-------------------------

* [biocorecrg/master_of_pores](https://github.com/biocorecrg/master_of_pores) - Nextflow pipeline for analysis of Nanopore data from direct RNA sequencing (see [also](https://biocorecrg.github.io/covid/)).

* [BU-ISCIII/SARS-Cov2_analysis](https://github.com/BU-ISCIII/SARS-Cov2_analysis) - SARS-Cov2 bioinformatics analysis.

* [connor-lab/ncov2019-artic-nf](https://github.com/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](https://github.com/heuermh/sars-cov-2) - Transform SARS-CoV-2 annotated genomes into sequences and features in [Apache Parquet](http://parquet.apache.org) format.

* [jnoms/virID](https://github.com/jnoms/virID) - Viral Identification and Discovery - A viral characterization pipeline built in Nextflow.

* [nf-core/viralrecon](https://github.com/nf-core/viralrecon/) - Assembly and intrahost/low-frequency variant calling for viral samples.

* [vtilloy/aspicov](https://gitlab.com/vtilloy/aspicov) - Automated and Standardized Pipeline for Identification of SARS-Cov2 nucleotidic Variants.

Other pipelines

------------------

* [abreschi/ShortRNA-nf](https://github.com/abreschi/ShortRNA-nf) - Pipeline for processing shortRNA-seq data.

* [andremrsantos/next-pipes-lghm](https://github.com/andremrsantos/next-pipes-lghm) - Eukaryotic genome annotation pipeline.

* [AveraSD/nextflow-kallisto](https://github.com/AveraSD/nextflow-kallisto)

* [AveraSD/nextflow-rnastar](https://github.com/AveraSD/nextflow-rnastar)

* [cbcrg/benchfam](https://github.com/cbcrg/benchfam)

* [cbcrg/grape-nf](https://github.com/cbcrg/grape-nf) - Yet another RNA-Seq pipeline (deprecated)

* [cerebis/meta-sweeper](https://github.com/cerebis/meta-sweeper) - Parametric sweep of simulated microbial communities and metagenomic sequencing.

* [charite/ngspipeline](https://github.com/charite/ngspipeline)

* [chrisquince/DESMAN](https://github.com/chrisquince/DESMAN) - De novo Extraction of Strains from MetAgeNomes.

* [evanfloden/concTree](https://github.com/evanfloden/concTree) - Creates consensus trees using alignment uncertainty from many MSAs.

* [evanfloden/lncRNA-Annotation-nf](https://github.com/evanfloden/lncRNA-Annotation-nf) - lncRNA Annotation Pipeline based on STAR, Cufflinks and FEELnc.

* [evanfloden/paraMSA](https://github.com/evanfloden/paraMSA/) - Multiple sequence alignments for phylogenetic trees and bootstrap support values.

* [evanfloden/tuxedo-nf](https://github.com/evanfloden/tuxedo-nf) - Nextflow implementation of the Tuxedo Suite of Tools.

* [evanfloden/vast-tools-nf](https://github.com/evanfloden/vast-tools-nf) - Nextflow Implementation of VAST-TOOLS for profiling alternative splicing events in RNA-Seq data.

* [fredericlemoine/rna-pipeline](https://github.com/fredericlemoine/rna-pipeline)

* [h3abionet/chipimputation](https://github.com/h3abionet/chipimputation) - Imputation workflow developed as part of the H3 Africa BioNet Hackathon.

* [h3abionet/h3agwas](https://github.com/h3abionet/h3agwas) - GWAS pipeline developed as part of the H3 Africa BioNet Hackathon.

* [HadrienG/pipelines](https://github.com/HadrienG/pipelines)

* [hmkim/workflow](https://github.com/hmkim/workflow/tree/master/nextflow)

* [holtgrewe/ngs_pipelines](https://github.com/holtgrewe/ngs_pipelines) - Nextflow-based pipelines for typical NGS processing tasks.

* [IARCbioinfo/bam_realignment-nf](https://github.com/IARCbioinfo/bam_realignment-nf)

* [IARCbioinfo/bametrics-nf](https://github.com/IARCbioinfo/bametrics-nf) - Compute average metrics from reads that overlap a given set of positions.

* [IARCbioinfo/GVCF_pipeline-nf](https://github.com/IARCbioinfo/GVCF_pipeline-nf)

* [IARCbioinfo/mpileup-nf](https://github.com/IARCbioinfo/mpileup-nf) - Coverage computation with samtools mpileup.

* [IARCbioinfo/mutect-nf](https://github.com/IARCbioinfo/mutect-nf)

* [InSilicoDB/pipeline-kallisto](https://github.com/InSilicoDB/pipeline-kallisto/)

* [InSilicoDB/snp-imputation-nf](https://github.com/InSilicoDB/snp-imputation-nf)

* [jdidion/rna-quick](https://github.com/jdidion/rna-quick) - Rapid analysis of gene and transcript quantification and differential expression.

* [joshua-d-campbell/nf-GATK_Exome_Preprocess](https://github.com/joshua-d-campbell/nf-GATK_Exome_Preprocess) - GATK best practice guide to preprocess whole exome sequencing (WES) data.

* [meissnert/nextflow-gtool](https://github.com/meissnert/nextflow-gtool)

* [CDCgov/mycosnp-nf](https://github.com/CDCgov/mycosnp-nf) - Portable workflow for performing whole genome sequencing analysis of fungal organisms.

* [NationalGenomicsInfrastructure/icing](https://github.com/NationalGenomicsInfrastructure/icing) - HLA typing from OxfordNanopore reads.

* [NBISweden/wgs-structvar](https://github.com/NBISweden/wgs-structvar) - Genome Sequenceing Structural Variation Pipelines.

* [MHH-RCUG/nf_wochenende](https://github.com/MHH-RCUG/nf_wochenende) - A metagenomic (and genomic) alignment and normalization pipeline for long and short reads

* [nmdp-bioinformatics/flow-blast-hml](https://github.com/nmdp-bioinformatics/flow-blast-hml)

* [nmdp-bioinformatics/flow-validation](https://github.com/nmdp-bioinformatics/flow-validation)

* [ODiogoSilva/innuca-nf](https://github.com/ODiogoSilva/innuca-nf) - A nextflow implementation of INNUENDO quality control of reads, de novo assembly and contigs quality assessment.

* [pbelmann/sra-download](https://github.com/pbelmann/sra-download)

* [CDCgov/PHoeNIx](https://github.com/CDCgov/phoenix) - A short-read pipeline for healthcare-associated and antimicrobial resistant pathogens.

* [PlantandFoodResearch/VariantAnalysis](https://github.com/PlantandFoodResearch/VariantAnalysis) - Bioinformatic variant calling pipeline.

* [robsyme/nextflow-annotate](https://github.com/robsyme/nextflow-annotate) - Fungal genome annotation workflow

* [robsyme/nextflow-mapping](https://github.com/robsyme/nextflow-mapping)

* [robsyme/workflows-proteogenomics](https://github.com/robsyme/workflows-proteogenomics) - Versioned, shareable and replicable workflows for proteogenomics.

* [CDCgov/SC2CLIA](https://github.com/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](https://github.com/skner/iasi-pipe)

* [snewhouse/ngs_nextflow](https://github.com/snewhouse/ngs_nextflow) - Alignment, Variant Calling, GATK Best Practices.

* [wittelab/orchid](https://github.com/Wittelab/orchid) - Novel management, annotation, and machine learning framework for analyzing cancer mutations.

Tutorials

----------

* [Bioinformatics pipeline example from the bottom up](https://ricomnl.com/blog/bottom-up-bioinformatics-pipeline/)

* [CRG course](https://github.com/nextflow-io/crg-course-nov16)

* [Introduction to Bioinformatics workflows with Nextflow and nf-core](https://carpentries-incubator.github.io/workflows-nextflow/)

* [Nextflow patterns](https://github.com/nextflow-io/patterns) - A collection of common Nextflow implementation patterns

* [Nextflow tutorial](https://github.com/nextflow-io/hack17-tutorial)

* [Nextflow training by Seqera Labs](https://training.seqera.io)

* [Nextflow demos](https://github.com/stevekm/nextflow-demos) - Example Nextflow pipelines and programming techniques

 (by Stephen Kelly)

* [H3ABioNet course](https://github.com/shaze/nextflow-course)

* [Running nf-core pipelines with AWS Batch](https://apeltzer.github.io/post/01-aws-nfcore/)

* [Running nextflow on AWS Batch](https://antunderwood.gitlab.io/bioinformant-blog/posts/running_nextflow_on_aws_batch/)

* [How to make a bigger custom AMI?](https://maxulysse.github.io/2018/11/05/Custom-AMI/)

* [Nextflow on AWS Batch](https://aws-samples.github.io/aws-genomics-workflows/orchestration/nextflow/nextflow-overview.html)

* [Pipelines on AWS](https://t-neumann.github.io/pipelines/AWS-pipeline/)

* [Reproducible, scalable, and shareable analysis workflows with Nextflow](https://sateeshperi.github.io/nextflow_varcal/nextflow/)

* [Running Nextflow on Google Cloud](https://cloud.google.com/life-sciences/docs/tutorials/nextflow)

* [Using AWS Batch to process 67,000 genomes with Bactopia](https://read-lab-confederation.github.io/blog/posts/bactopia-aws-and-67000-genomes/)

Pipelines collections

-------------

* [IARC-nf](https://github.com/IARCbioinfo/IARC-nf) - List of [IARC](https://www.iarc.fr/) bioinformatics nextflow pipelines.

* [nf-core](http://nf-co.re/pipelines) - A collection of high quality Nextflow pipelines.

Modules collections

--------------------

* [biocorecrg/BioNextflow](https://github.com/biocorecrg/BioNextflow) - Repository to host DSL2 based tool-specific sub-workflows 

* [nf-core/modules](https://github.com/nf-core/modules/) - Repository to host tool-specific module files for the Nextflow DSL2 community

* [UMCUGenetics/NextflowModules](https://github.com/UMCUGenetics/NextflowModules) - UMCU Genetics Nextflow modules

Presentations

-------------

* [rsuchecki.github.io](https://rsuchecki.github.io/reproducible/show.html#/) - Reproducible and Reusable publication and analysis workflow by [bioinforad](https://twitter.com/bioinforad)

* [CIC Show-and-Tell](https://cdn.rawgit.com/robsyme/nextflow-intro/4615e5a/index.html) - Nice Nextflow presentation by [@robsyme](https://github.com/robsyme)

Video

-----

* [Nextflow: Scalable, Shareable & Reproducible workflows](https://www.youtube.com/watch?v=lqm-VV5dOgk) - Awesome intro by Rad Suchecki

* [Nextflow Youtube channel](https://www.youtube.com/channel/UCB-5LCKLdTKVn2F4V4KlPbQ)

* [Using NextFlow pipelines at Babraham](https://www.youtube.com/watch?v=oAjZ0xmewp8)

Syntax highlighting

-------------------

* [Atom](https://atom.io/packages/language-nextflow)

* [Emacs](https://github.com/Emiller88/nextflow-mode)

* [Sublime Text](https://github.com/peterk87/sublime-nextflow)

* [VIM](https://github.com/LukeGoodsell/nextflow-vim)

* [VSCode](https://github.com/nextflow-io/vscode-language-nextflow)

Other links  

---------------

* [Nextflow Hackathon '17](https://github.com/nextflow-io/hack17) - Projects repositorty of the Nextflow Hackathon held in Barcelona, Sept 2017

* [Nextflow Workbench](http://campagnelab.org/software/nextflow-workbench/) - Workbench that make it easier to write data analysis workflows with Nextflow

* [nf-core/tools](https://github.com/nf-core/tools) - Helper tools for the nf-core community, linting, template...

* [Make to Nextflow](https://github.com/lindenb/xml-patch-make/wiki/Tabix) - Converts Makefile to Nextflow

* [NCBI-Hackathons/SPeW](https://github.com/NCBI-Hackathons/SPeW) - A discussion comparting different workflow frameworks including Nextflow.

* [NGS workflow](https://jmazz.me/blog/NGS-Workflows) Excellent blog post comparing Make/Snakemake/Nextflow by Julian Mazzitelli