nextflow

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nextflow-io /nextflow

Star3.2k

A DSL for data-driven computational pipelines

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

UpdatedNov 28, 2025
Groovy

nf-core /rnaseq

Star1.2k

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

workflow rna-seq pipeline nextflow rna nf-core

UpdatedNov 28, 2025
Nextflow

nextflow-io /awesome-nextflow

Star613

A curated list of nextflow based pipelines

nextflow awesome-list

UpdatedJun 23, 2025

nf-core /sarek

Star503

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

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

UpdatedNov 27, 2025
Nextflow

bactopia /bactopia

Star488

A flexible pipeline for complete analysis of bacterial genomes

nextflow conda bioconda bacterial-genomes fastqs

UpdatedNov 27, 2025
Nextflow

nf-core /modules

Star387

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

modules nextflow pipelines workflows nf-core dsl2 nf-test

UpdatedNov 28, 2025
Nextflow

nextflow-io /patterns

Star366

A curated collection of Nextflow implementation patterns

nextflow

UpdatedNov 21, 2023
Nextflow

nf-core /scrnaseq

Star302

Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection

workflow rna-seq pipeline nextflow single-cell kallisto 10x-genomics 10xgenomics nf-core bustools alevin cellranger star-solo

UpdatedNov 25, 2025
Nextflow

nf-core /tools

Star282

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

python workflow bioinformatics pipeline nextflow linting linter nf-core

UpdatedNov 27, 2025
Python

lynnlangit /gcp-for-bioinformatics

Star280

GCP for Bioinformatics Researchers

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

UpdatedMay 29, 2025
Jupyter Notebook

nf-core /mag

Star254

Assembly and binning of metagenomes

workflow bioinformatics nanopore pipeline annotation nextflow assembly metagenomics binning metagenomes nanopore-sequencing nf-core long-read-sequencing

UpdatedNov 28, 2025
Nextflow

assemblerflow /flowcraft

Star244

FlowCraft: a component-based pipeline composer for omics analysis using Nextflow. 🐳📦

pipeline genomics nextflow bacterial

UpdatedAug 10, 2025
Python

nvuillam /npm-groovy-lint

Sponsor

Star239

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

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

UpdatedNov 29, 2025
JavaScript

nf-core /chipseq

Star226

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

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

UpdatedNov 21, 2025
Nextflow

nf-core /ampliseq

Star225

Amplicon sequencing analysis workflow using DADA2 and QIIME2

workflow pipeline nextflow metagenomics pacbio edna microbiome iontorrent illumina metabarcoding 16s rrna its 18s taxonomic-classification amplicon-sequencing qiime2 nf-core taxonomic-profiling metataxonomics

UpdatedNov 20, 2025
Nextflow

nf-core /atacseq

Star217

ATAC-seq peak-calling and QC analysis pipeline

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

UpdatedNov 20, 2025
Nextflow

nf-core /nanoseq

Star215

Nanopore demultiplexing, QC and alignment pipeline

workflow nanopore pipeline nextflow alignment qc demultiplexing nf-core

UpdatedNov 20, 2025
Nextflow

nextflow-io /training

Star203

Nextflow training material

training learning tutorial workshop nextflow pipelines teaching workflows

UpdatedNov 26, 2025
Nextflow

nf-core /eager

Star186

A fully reproducible and state-of-the-art ancient DNA analysis pipeline

workflow bioinformatics pipeline genome nextflow metagenomics population-genetics adna pathogen-genomics nf-core ancientdna ancient-dna-analysis

UpdatedNov 21, 2025
Nextflow

lynnlangit /aws-for-bioinformatics

Star183

AWS for Bioinformatics Researchers

aws bioinformatics ec2 athena genomics nextflow aws-batch sagemaker awsbatch

UpdatedJul 17, 2025
Jupyter Notebook

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nextflow

Here are 929 public repositories matching this topic...

nextflow-io /nextflow

nf-core /rnaseq

nextflow-io /awesome-nextflow

nf-core /sarek

bactopia /bactopia

nf-core /modules

nextflow-io /patterns

nf-core /scrnaseq

nf-core /tools

lynnlangit /gcp-for-bioinformatics

nf-core /mag

assemblerflow /flowcraft

nvuillam /npm-groovy-lint

nf-core /chipseq

nf-core /ampliseq

nf-core /atacseq

nf-core /nanoseq

nextflow-io /training

nf-core /eager

lynnlangit /aws-for-bioinformatics

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