Projects in Awesome Lists tagged with nextflow

https://github.com/nextflow-io/nextflow

A DSL for data-driven computational pipelines

aws bioinformatics cloud dataflow docker groovy hello hpc nextflow pipeline pipeline-framework reproducible-research reproducible-science sge singularity singularity-containers slurm workflow-engine

Last synced: 13 May 2025

https://github.com/nf-core/rnaseq

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

nextflow nf-core pipeline rna rna-seq workflow

Last synced: 27 Feb 2026

https://github.com/bactopia/bactopia

A flexible pipeline for complete analysis of bacterial genomes

bacterial-genomes bioconda conda fastqs nextflow

Last synced: 04 Apr 2026

https://github.com/nf-core/sarek

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

annotation bioinformatics cancer conda containers gatk4 genomics germline next-generation-sequencing nextflow nf-core pipeline pre-processing reproducible-research somatic target-panels variant-calling whole-exome-sequencing whole-genome-sequencing workflow

Last synced: 12 Feb 2026

https://github.com/nextflow-io/patterns

A curated collection of Nextflow implementation patterns

nextflow

Last synced: 28 Jan 2026

https://github.com/nf-core/modules

Repository to host tool-specific module files for the Nextflow DSL2 community!

dsl2 modules nextflow nf-core nf-test pipelines workflows

Last synced: 16 Jan 2026

https://github.com/lynnlangit/gcp-for-bioinformatics

GCP for Bioinformatics Researchers

bioinformatics bioinformatics-analysis bioinformatics-pipeline bioinformatics-researchers gcp genomics google google-batch nextflow

Last synced: 16 May 2025

https://github.com/nvuillam/npm-groovy-lint

Lint, format and auto-fix your Groovy / Jenkinsfile / Gradle files using command line

ci code-quality-analyzer codenarc gradle groovy groovy-language hacktoberfest jenkinsfile lint linter megalinter nextflow sarif sarif-report

Last synced: 02 Apr 2026

https://github.com/assemblerflow/flowcraft

FlowCraft: a component-based pipeline composer for omics analysis using Nextflow. :whale::package:

bacterial genomics nextflow pipeline

Last synced: 14 Jan 2026

https://github.com/nf-core/tools

Python package with helper tools for the nf-core community.

bioinformatics linter linting nextflow nf-core pipeline python workflow

Last synced: 16 Jan 2026

https://github.com/nextflow-io/training

Nextflow training material

learning nextflow pipelines teaching training tutorial workflows workshop

Last synced: 03 Feb 2026

https://github.com/nf-core/chipseq

ChIP-seq peak-calling, QC and differential analysis pipeline.

chip chip-seq chromatin-immunoprecipitation macs2 nextflow nf-core peak-calling pipeline workflow

Last synced: 16 Jan 2026

https://github.com/nf-core/nanoseq

Nanopore demultiplexing, QC and alignment pipeline

alignment demultiplexing nanopore nextflow nf-core pipeline qc workflow

Last synced: 16 Jan 2026

https://github.com/nf-core/atacseq

ATAC-seq peak-calling and QC analysis pipeline

atac-seq chromatin-accessibiity nextflow nf-core pipeline workflow

Last synced: 16 Jan 2026

https://github.com/askimed/nf-test

Simple test framework for Nextflow pipelines

nextflow test-automation testing testing-tools

Last synced: 15 Jan 2026

https://github.com/pgscatalog/pgsc_calc

The Polygenic Score Catalog Calculator is a nextflow pipeline for polygenic score calculation

genetic-risk-score nextflow pgs pgs-catalog polygenic-risk-score polygenic-risk-scores polygenic-score polygenic-scores prs workflow

Last synced: 10 Mar 2026

https://github.com/lynnlangit/aws-for-bioinformatics

AWS for Bioinformatics Researchers

athena aws aws-batch awsbatch bioinformatics ec2 genomics nextflow sagemaker

Last synced: 19 Apr 2025

https://github.com/EBI-Metagenomics/emg-viral-pipeline

VIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies

cwl nextflow pipeline viruses workflow

Last synced: 09 May 2025

https://github.com/dockstore/dockstore

An app store for scientific workflows, tools, notebooks, and services

bioinformatics containers cwl docker dockstore nextflow wdl workflow

Last synced: 20 Jan 2026

https://github.com/stevekm/nextflow-demos

Example Nextflow pipelines and programming techniques

nextflow

Last synced: 08 Oct 2025

https://github.com/bastidanicolas/nextauth-prisma-stripe

How to integrate subscriptions into your Next.js project (/app). The tutorial utilizes Next.js (v13.4) with the /app directory structure, NextAuth v4 for authentication, Prisma for database management, and Stripe for payment processing.

auth authentication google-authentication mysql-database next-auth next-auth-adapter next-js nextflow nextjs nextjs13 nextjs14 prisma prisma-client route-protection stripe stripe-subscriptions subscription subscriptions-and-payments

Last synced: 01 Oct 2025

https://github.com/nf-core/configs

Config files used to define parameters specific to compute environments at different Institutions

bioinformatics configuration nextflow nf-core pipelines workflows

Last synced: 16 Jan 2026

https://github.com/fmalmeida/bacannot

Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.

annotation antimicrobial-genes-annotation barrnap genome-analysis genome-browser genomic-islands-prediction insertion-sequences ko-annotation methylation-annotation mobile-genetic-elements nextflow phigaro pipeline prophage-sequences-prediction prophages reproducible-research rgi rrna-prediction virulence-factor virulence-genes

Last synced: 05 May 2025

https://github.com/replikation/What_the_Phage

WtP: Phage identification via nextflow and docker or singularity

bioinformatics nextflow nextflow-pipelines phage-identification phage-sequences phages

Last synced: 09 Jul 2025

https://github.com/open2c/distiller-nf

A modular Hi-C mapping pipeline

hi-c nextflow pipeline

Last synced: 09 Jul 2025

https://github.com/cdcgov/mycosnp-nf

MycoSNP: Whole Genome Sequencing Analysis of Fungal Isolates

myco nextflow nf-core snp

Last synced: 05 Feb 2026

https://github.com/nvuillam/vscode-groovy-lint

VSCode extension to lint , correct and format groovy and Jenkinsfile

code-quality-analyzer codenarc gradle groovy groovy-language jenkinsfile linter nextflow vscode vscode-extension

Last synced: 15 Apr 2026

https://github.com/likelet/lncpipe

A Nextflow-based pipeline for comprehensive analyses of long non-coding RNAs from RNA-seq datasets

lncrnas nextflow pipeline

Last synced: 24 Apr 2025

https://github.com/gluonfield/nf-shard

Nextflow runs monitoring and organisation UI

nextflow nf-shard nf-tower

Last synced: 04 Sep 2025

https://github.com/nextflow-io/rnaseq-nf

A proof of concept of RNAseq pipeline

genomics nextflow rnaseq

Last synced: 09 Aug 2025

https://github.com/genepi/nf-gwas

A nextflow pipeline to perform state-of-the-art genome-wide association studies.

gwas imputation nextflow regenie singularity slurm

Last synced: 02 Feb 2026

https://github.com/danrlu/nextflow_cheatsheet

Tips for Nextflow and cheatsheet for channel operation

cheatsheet nextflow tips

Last synced: 05 Mar 2026

https://github.com/nf-core/website

Code and files for the main nf-core website.

nextflow nf-core website

Last synced: 16 Jan 2026

https://github.com/lumc/pytest-workflow

Configure workflow/pipeline tests using yaml files.

cromwell miniwdl nextflow pipeline pytest pytest-plugin snakemake test testing wdl wdl-devtools workflow workflow-testing yaml

Last synced: 08 Apr 2025

https://github.com/nf-core/pangenome

Renders a collection of sequences into a pangenome graph.

nextflow nf-core pangenome pipeline workflow

Last synced: 16 Jan 2026

https://github.com/brwnj/covviz

Multi-sample genome coverage viewer to observe large, coverage-based anomalies alongside annotations and sample metadata

coverage genomics-visualization nextflow

Last synced: 08 Mar 2026

https://brwnj.github.io/covviz/

Multi-sample genome coverage viewer to observe large, coverage-based anomalies alongside annotations and sample metadata

coverage genomics-visualization nextflow

Last synced: 18 Nov 2025

https://github.com/mribeirodantas/nextflowsnippets

This repository hosts a large collection of Nextflow snippets

nextflow nextflow-language pipeline programming snippets workflow

Last synced: 06 Jan 2026

https://github.com/uphl-biongs/cecret

Reference-based consensus creation

amplicon bioinformatics monkeypox nextflow sars-cov-2

Last synced: 10 Feb 2026

https://github.com/nf-core/epitopeprediction

A bioinformatics best-practice analysis pipeline for epitope prediction and annotation

epitope epitope-prediction mhc-binding-prediction nextflow nf-core pipeline workflow

Last synced: 02 Mar 2026

https://github.com/nextflow-io/nf-validation

Params validation plugin for Nextflow pipelines

json-schema nextflow plugin samplesheet validation

Last synced: 09 Apr 2025

https://github.com/nbisweden/pipelines-nextflow

A set of workflows written in Nextflow for Genome Annotation.

genome-annotation nextflow workflow

Last synced: 18 Jul 2025

https://github.com/seqeralabs/wave

On-demand containers provisioning service

containers docker kubernetes nextflow singularity

Last synced: 17 Mar 2026

https://github.com/gregor-mendel-institute/aradeepopsis

A versatile, fully open-source pipeline to extract phenotypic measurements from plant images

arabidopsis-thaliana deep-learning nextflow plant-phenotyping scikit-image semantic-segmentation tensorflow

Last synced: 21 Jun 2025

https://github.com/Gregor-Mendel-Institute/aradeepopsis

A versatile, fully open-source pipeline to extract phenotypic measurements from plant images

arabidopsis-thaliana deep-learning nextflow plant-phenotyping scikit-image semantic-segmentation tensorflow

Last synced: 07 May 2025

https://github.com/bentsherman/nf-boost

Experimental features for Nextflow

nextflow

Last synced: 14 Apr 2025

https://github.com/midnighter/nextflow-gotchas

A collection of unexpected challenges and learnings with nextflow and nf-core.

gotcha nextflow nextflow-pipeline nextflow-process nextflow-workflow nf-core

Last synced: 13 May 2025

https://github.com/nextflow-io/vscode-language-nextflow

Nextflow language support for Visual Studio Editor

nextflow vscode-extension

Last synced: 29 Apr 2026

https://github.com/fmalmeida/ngs-preprocess

A pipeline for preprocessing NGS data from Illumina, Nanopore and PacBio technologies

bax2bam bioinformatics illumina nanopack nextflow ngs ngs-preprocess pacbio pacbio-ccs pipeline porechop reproducible-research reproducible-science trimgalore workflow

Last synced: 22 Jan 2026

https://github.com/janeliascicomp/multifish

EASI-FISH analysis pipeline for spatial transcriptomics

easi-fish ibm-platform-lsf nextflow pipeline

Last synced: 15 Apr 2025

https://github.com/nextflow-io/nf-hack17-tutorial

Nextflow basic tutorial for newbie users

bioinformatics docker genomics nextflow singularity tutorial

Last synced: 06 May 2025

https://github.com/JaneliaSciComp/multifish

EASI-FISH analysis pipeline for spatial transcriptomics

easi-fish ibm-platform-lsf nextflow pipeline

Last synced: 16 Apr 2025

https://github.com/sanger-tol/treeval

Pipelines for the production of Treeval data

curation genome-alignment genome-assembly genomics nextflow pipeline quality-control synteny

Last synced: 07 Apr 2026

https://github.com/beiko-lab/arete

AMR/VF LGT focused bacterial genomics analysis workflow

antimicrobial-genes-annotation antimicrobial-resistance bacterial-genome-analysis genomic-islands-prediction lateral-gene-transfer metagenomics mobile-genetic-elements nextflow pangenomics pipeline poppunk recombination reproducible-research rgi virulence-factor

Last synced: 11 Mar 2026

https://github.com/cdcgov/tostadas

🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission

azure bioinformatics conda docker genbank genetics liftoff metadata mpox ncbi nextflow nf-tower pipeline python rna-seq scicomp sequencing singularity sra vadr

Last synced: 15 Apr 2025

https://github.com/carpentries-incubator/workflows-nextflow

Workflow management with Nextflow and nf-core

bulk-rna-seq carpentries-incubator english lesson nextflow nf-core pre-alpha rna-seq-analysis workflow-management

Last synced: 25 Jan 2026

https://github.com/sanger-tol/genomenote

Nextflow DSL2 pipeline to generate a Genome Note, including assembly statistics, quality metrics, and Hi-C contact maps. This workflow is part of the Tree of Life production suite.

genomics hic nextflow pipeline publications statistics

Last synced: 17 Jan 2026

https://github.com/telatin/nextflow-example

A simple DSL2 workflow: tutorial

denovo-assembly nextflow nextflow-dsl2 tutorial tutorial-code workflow

Last synced: 22 Feb 2026

https://github.com/peterk87/sublime-nextflow

Nextflow workflow syntax highlighting and snippets for Sublime Text 4

editor-plugin nextflow nextflow-dsl2 nextflow-workflow snippets sublime-text sublime-text-3 sublime-text-4 syntax-highlighting

Last synced: 14 Jan 2026

https://github.com/sanger-tol/genomeassembly

Implementation of ToL genome assembly workflows

genome-assembly genomics nextflow pipeline

Last synced: 17 Jan 2026

https://github.com/brwnj/idplot

compare sequences to a shared root reference sequence.

fasta nextflow plotly recombination sars-cov-2 virus

Last synced: 10 Mar 2026

https://github.com/nextflow-io/crg-course-nov16

Nextflow + Docker tutorial material

nextflow

Last synced: 03 Mar 2025

https://github.com/biocorecrg/MOP2

Master of Pores 2

cdna docker nanopore nextflow pipeline rna rna-seq singularity

Last synced: 06 May 2025

https://github.com/nextflow-io/hyperopt

Nextflow pipeline for hyperparameter optimization of machine learning models

machine-learning nextflow

Last synced: 28 Jun 2025

https://github.com/GoekeLab/bambu-pipe

Transcript discovery and quantification for long read single cell and spatial transcriptomics data using Bambu

bambu genomics isoform-quantification long-read-rna-seq long-read-sequencing nanopore nextflow pacbio pipeline rna-seq single-cell spatial-transcriptomics transcript-discovery transcript-quantification transcriptomics

Last synced: 11 Jun 2026

https://github.com/nextflow-io/hello

Classic hello world script in Nextflow language

hello-world nextflow

Last synced: 16 Feb 2026

https://github.com/juke34/aline

Nextflow Alignment Pipeline - from fastq.gz to sorted bam/cram with ease

bbmap bowtie bowtie2 bwa bwamem2 dragmap graphmap2 hisat2 kallisto last minimap2 nextflow ngmlr novoalign nucmer salmon star starlong sublong subread

Last synced: 18 Feb 2026

https://github.com/seqeralabs/wave-showcase

Examples showing how to configure Nextflow to run with Wave containers provisioning service

containers docker nextflow

Last synced: 15 Feb 2026

https://github.com/edmundmiller/nextflow-mode

Emacs major mode for Nextflow

emacs emacs-mode emacs-package hacktoberfest nextflow

Last synced: 15 Sep 2025

https://github.com/angelovangel/nxf-kraken2

A simple nextflow pipeline for running kraken2 and bracken in a docker container

bracken kraken2 metagenomics nextflow pipeline

Last synced: 13 Feb 2026

https://github.com/nf-core/nascent

Nascent Transcription Processing Pipeline

gro-seq nascent nextflow nf-core pipeline pro-seq rna transcription tss workflow

Last synced: 16 Jan 2026

https://github.com/nextflow-io/language-server

The Nextflow language server

language-server-protocol nextflow

Last synced: 10 Jun 2025

https://github.com/guigolab/chip-nf

An automated ChIP-seq pipeline using Nextfow

chip-seq crg guigo guigolab-nf nextflow ngs pipeline

Last synced: 14 Jan 2026

https://github.com/guigolab/fa-nf

Functional annotation pipeline for proteins from non-model organisms implemented in Nextflow

bioinformatics nextflow pipeline

Last synced: 21 Jan 2026

https://github.com/dockstore/dockstore-ui2

Website user interface for Dockstore in Angular2

angular cwl dockstore hacktoberfest nextflow wdl

Last synced: 20 Jan 2026

https://github.com/sydney-informatics-hub/bioinformatics

A suite of bioinformatics data processing and analysis pipelines, software, and training resources for common methods.

bioinformatics bioinformatics-analysis bioinformatics-pipeline bioinformatics-scripts cancer genomics germline-variants indels metagenomics nextflow nextflow-pipelines ngs research-computing rnaseq snps somatic-variants sydney-informatics-hub transcriptomics variant-calling

Last synced: 11 Feb 2026

https://github.com/nf-core/viralintegration

Analysis pipeline for the identification of viral integration events in genomes using a chimeric read approach.

chimeric-alignment ctat nextflow nf-core pipeline viral-integration virus virusintegrationfinder workflow

Last synced: 16 Jan 2026

https://github.com/mahesh-panchal/nf-cascade

A proof of concept daisy-chaining Nextflow workflows

nextflow nextflow-pipeline nextflow-workflow

Last synced: 24 Dec 2025

https://github.com/sanger-tol/blobtoolkit

Nextflow DSL2 pipeline to generate data for a BlobToolKit analysis. This workflow is part of the Tree of Life production suite.

blobtools decontamination genomehubs genomics nextflow pipeline workflow

Last synced: 12 Feb 2026

https://github.com/bigbio/nf-workflows

Repository of Nextflow+BioContainers workflows

biocontainers bioinformatics bioinformatics-pipeline nextflow proteomics workflow

Last synced: 17 Jan 2026

https://github.com/dincalcilab/samurai

A bioinformatics best-practice analysis pipeline for the analysis of shallow whole genome sequencing (sWGS) data for the identification of copy number alterations (CNAs).

bioinformatics bioinformatics-pipeline nextflow nextflow-pipeline

Last synced: 02 Mar 2026