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

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

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

A single-cell RNAseq pipeline for 10X genomics data

Pipeline to fetch metadata and raw FastQ files from public databases

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

Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data

Assembly and intrahost/low-frequency variant calling for viral samples

WtP: Phage identification via nextflow and docker or singularity

Nextflow training material for introductory tutorial

A repository of pipelines for single-cell data in Nextflow DSL2

nextNEOpi: a comprehensive pipeline for computational neoantigen prediction

Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq

Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.

A flexible Nextflow-based framework for the definition of sequencing data processing pipelines

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

Please consider using/contributing to https://github.com/nf-core/sarek

Proteomics label-free quantification (LFQ) analysis pipeline

Identify and quantify MHC eluted peptides from mass spectrometry raw data

Differential gene expression analysis and pathway analysis of RNAseq data

A single cell transcriptomics pipeline for QC, integration and making the data presentable

UMCU Genetics Nextflow modules

Comprehensive pipeline for donor demultiplexing in single cell

Please consider using/contributing to https://github.com/nf-core/scdownstream

Customer workshop materials

Automated quantitative analysis of DIA proteomics mass spectrometry measurements.

Nextflow pipeline wrapper for executing Cell Ranger

Easy & parallel download of FASTQ files from public repositories (SRA, EGA, GDC)

Genome Diagnostics Nextflow WES workflow

DEPRECATED | pySCENIC pipeline implemented in Nextflow using containers