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references

riboseq

Pipeline for the analysis of ribosome profiling, or Ribo-Seq (also named ribosome footprinting) data.

rnadnavar

Pipeline for RNA and DNA integrated analysis for somatic mutation detection

rnafusion

RNA-seq analysis pipeline for detection gene-fusions

rnaseq

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

rnasplice

rnasplice is a bioinformatics pipeline for RNA-seq alternative splicing analysis

rnavar

gatk4 RNA variant calling pipeline

sammyseq

Pipeline for Sequential Analysis of MacroMolecules accessibilitY sequencing (SAMMY-seq) data, to analyze chromatin state.

sarek

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

scflow

Complete analysis workflow for single-cell/nuclei RNA-sequencing data.

scrnaseq

A single-cell RNAseq pipeline for 10X genomics data

setup-nextflow

slamseq

SLAMSeq processing and analysis pipeline

smartseq2

A pipeline for processing single cell RNA-seq data generated with the SmartSeq2 protocol.

smrnaseq

A small-RNA sequencing analysis pipeline

spatialtranscriptomics

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

spinningjenny

Pipeline for simulating the first industrial revolution using Agent Based Models.

ssds

Single-stranded DNA Sequencing (SSDS) nf-core pipeline

sublime

Nextflow workflow syntax highlighting and snippets for Sublime Text 4

taxprofiler

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

test-datasets

Test data to be used for automated testing with the nf-core pipelines

testpipeline

A small example pipeline used to test new nf-core infrastructure and common code.

tools

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

tower-action

GitHub Action to launch a workflow using Nextflow Tower.

vale

Spelling and grammar linting for nf-core documentation

variantbenchmarking

A nextflow variant benchmarking pipeline - premature

variantcatalogue

Pipeline to generate variant catalogues, a list of variants and their frequencies in a population, from whole genome sequences.

vipr

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

viralintegration

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

viralrecon

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