nf-core

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

A bioinformatics best-practice processing and quality control pipeline for Xenium and Artera data

Pipeline for the identification of extrachromosomal circular DNA (ecDNA) from Circle-seq, WGS, and ATAC-seq data that were generated from cancer and other eukaryotic cells.

Image Mass Cytometry analysis pipeline

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

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

A repository for hosting Nextflow DSL2 module files containing tool-specific process definitions and their associated documentation for MSKCC

This pipeline is dedicated to identifying the most stable genes within a single or multiple expression dataset(s). This is particularly useful for identifying the most suitable RT-qPCR reference genes for a specific species.

Nextflow config builder scripts for supported HPC infrastructures.

Nextflow workflow syntax highlighting and snippets for Sublime Text 4

The pipeline performs a comprehensive quality control of mass spectrometry-based proteomics experiments.

A pipeline for characterising the Human Blood Group and Red Cell Antigens using Oxford Nanopore third-generation sequencing data.

Work packages 3 (Land Taxonomy Classifier) and 4 (Outlier and Data-Quality Detection Service) on BiodivPipeline: A Modular nf-core Workflow for FAIR Biodiversity Data Processing

A pipeline for detecting MRD using capture based assay

An agentic bioinformatics analyst: it runs the analysis on your own compute, self-heals failures, verifies the output, and returns a reproducible result.

nf-core in numbers

SLURM execution wrapper and configuration layer for nf-core/rnaseq used in viral RNA-seq projects.

Reusable Nextflow subworkflow for auditable AI-assisted variant triage

Processing of RNA-Seq data with nf-core pipelines and machine learning

End-to-end benchmarking and validation of nf-core meta-omics pipelines, testing how real multi-omics datasets can be chained across pipelines through reproducible samplesheet handoffs.