nextflow

A DSL for data-driven computational pipelines

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

A curated list of nextflow based pipelines

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

A flexible pipeline for complete analysis of bacterial genomes

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

A curated collection of Nextflow implementation patterns

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

GCP for Bioinformatics Researchers

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

Assembly and binning of metagenomes

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

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

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

Amplicon sequencing analysis workflow using DADA2 and QIIME2

Nanopore demultiplexing, QC and alignment pipeline

ATAC-seq peak-calling and QC analysis pipeline

Nextflow training material

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

Pipeline to fetch metadata and raw FastQ files from public databases