nf-core-utils
Contributor
A Nextflow plugin providing utility functions used by nf-core pipelines, including genome attribute resolution, reference file management, and pipeline initialization.
nf-core/seqinspector
Developer and maintainer
A dedicated QC-only pipeline for sequencing data, performing subsampling, quality assessment, duplication analysis, and contamination detection with flexible MultiQC reporting.
nft-utils
Maintainer
An nf-test plugin providing additional functions and assertions for snapshot testing, including Nextflow version removal, YAML filtering, and channel utilities.
nf-core/createpanelrefs
Developer and maintainer
A helper pipeline to create panel of normals and other models for tools like Mutect2, GENS, CNVKit, and GATK's germlinecnvcaller.
nf-core/references
Developer and maintainer
A pipeline to build reference files for common organisms, including indices for BWA, STAR, HISAT2, Salmon, and more, with cloud storage similar to AWS iGenomes.
annotation-cache
Developer and maintainer
A resource providing pre-built SnpEff and VEP annotation caches on S3, with pipelines to download and manage caches for the nf-core community.
nf-core/fetchngs
Maintainer
A bioinformatics pipeline to fetch metadata and raw FastQ files from public sequencing databases, supporting SRA, ENA, DDBJ, and GEO identifiers.
nf-core/demultiplex
Maintainer
A pipeline to demultiplex the raw data produced by next generation sequencing machines, supporting Illumina, Element Biosciences, Singular Genomics, and 10x Genomics platforms, as well as FASTQ files with user supplied read structures.
nf-core
Core team member
A community effort to collect a curated set of analysis pipelines built using Nextflow. Provides standards, templates, tools, and CI testing for bioinformatics pipelines.
nf-core/rnafusion
Contributor
An open-source Nextflow pipeline for detecting fusion genes from RNA-seq data. Runs multiple fusion detection tools and generates a consolidated final report.
nf-core/sarek
Developer and maintainer
A portable workflow for whole-genome sequencing analysis of germline and somatic variants. Supports SNVs, indels, structural variants, CNVs, microsatellite instability, and annotation.
Interactome-Transcriptome Integration
Developer
A method to analyze gene expression data by superimposition of large-scale protein-protein interaction data over gene expression datasets for biomarker discovery in breast cancer.