nf-core

chipseq

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

bactmap

A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences

lncpipe

UNDER DEVELOPMENT--- Analysis of long non-coding RNAs from RNA-seq datasets

kmermaid

k-mer similarity analysis pipeline

clipseq

CLIP sequencing analysis pipeline for QC, pre-mapping, genome mapping, UMI deduplication, and multiple peak-calling options.

genomeassembler

diaproteomics

Automated quantitative analysis of DIA proteomics mass spectrometry measurements.

tower-action

GitHub Action to launch a workflow using Nextflow Tower.

fastquorum

Pipeline to produce consensus reads using unique molecular indexes/barcodes (UMIs)

cageseq

CAGE-sequencing analysis pipeline with trimming, alignment and counting of CAGE tags.

mnaseseq

MNase-seq analysis pipeline using BWA and DANPOS2.

pathogensurveillance

Surveillance of pathogens using population genomics and sequencing

denovohybrid

UNDER CONSTRUCTION: Hybrid genome assembly pipeline using a combination of long and short sequencing reads

molkart

A pipeline for processing Molecular Cartography data from Resolve Bioscience (combinatorial FISH)

datasync

nf-core/datasync is a system operation pipeline that provides several workflows for handling system operation / automation tasks

crisprvar

[WIP] Evaluate outcomes from genome editing experiments

prettier-plugin-nextflow

ddamsproteomics

Quantitative shotgun MS proteomics

gh-actions-lint

GitHub Action to run nf-core code linting on a Nextflow pipeline

logos

Host nf-core logos and templates for making new logos

rangeland

Pipeline for remotely sensed imagery. The pipeline processes satellite imagery alongside auxiliary data in multiple steps to arrive at a set of trend files related to land-cover changes.

sublime

Nextflow workflow syntax highlighting and snippets for Sublime Text 4

testpipeline

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

actions-runners

Instructions and scripts for custom GitHub Actions runners

callingcards

A pipeline for processing calling cards data

ssds

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

.github

Files for the @nf-core GitHub organisation

basic_training

Hosts the content of the basic nf-core training on how to create nf-core pipelines with `nf-core create`

liverctanalysis

UNDER CONSTRUCTION: pipeline for liver CT analysis

vale

Spelling and grammar linting for nf-core documentation