nf-core

A community effort to collect a curated set of analysis pipelines built using Nextflow.

Pinned Repositories

ampliseq
Amplicon sequencing analysis workflow using DADA2 and QIIME2
Language:Nextflow217 165 387143
chipseq
ChIP-seq peak-calling, QC and differential analysis pipeline.
Language:Nextflow221 162 206159
configs
Config files used to define parameters specific to compute environments at different Institutions
Language:Nextflow103 179 50327
mag
Assembly and binning of metagenomes
Language:Nextflow247 182 326137
modules
Repository to host tool-specific module files for the Nextflow DSL2 community!
Language:Nextflow374 210 2.4k902
proposals
Where new ideas for nf-core pipelines, special interest groups and more are proposed
8 11 503
rnaseq
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
Language:Nextflow1.1k 173 743794
sarek
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
Language:Nextflow478 149 819477
scrnaseq
Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection
Language:Nextflow289 156 200196
tools
Python package with helper tools for the nf-core community.
Language:Python268 165 1.2k208

nf-core's Repositories

nf-core/pangenome
Renders a collection of sequences into a pangenome graph. https://doi.org/10.1093/bioinformatics/btae609.
Language:Nextflow96 81 7120
nf-core/rnasplice
rnasplice is a bioinformatics pipeline for RNA-seq alternative splicing analysis
Language:Nextflow57 171 5536
nf-core/readsimulator
A pipeline to simulate sequencing reads, such as Amplicon, Target Capture, Metagenome, and Whole genome data.
Language:Nextflow32 169 138
nf-core/gwas
UNDER CONSTRUCTION: A pipeline for Genome Wide Association Studies
Language:Nextflow26 184 1025
nf-core/hgtseq
A pipeline to investigate horizontal gene transfer from NGS data
Language:Nextflow26 176 47
nf-core/imcyto
Image Mass Cytometry analysis pipeline
Language:Python25 138 718
nf-core/metaboigniter
Pre-processing of mass spectrometry-based metabolomics data with quantification and identification based on MS1 and MS2 data.
Language:Nextflow23 63 2416
nf-core/nascent
Nascent Transcription Processing Pipeline
Language:Nextflow19 175 6711
nf-core/denovotranscript
A pipeline for de novo transcriptome assembly of paired-end short reads from bulk RNA-seq
Language:Nextflow15 173 84
nf-core/tumourevo
Analysis pipleine to model tumour clonal evolution from WGS data (driver annotation, quality control of copy number calls, subclonal and mutational signature deconvolution)
Language:Nextflow14 8 135
nf-core/phageannotator
Pipeline for identifying, annotation, and quantifying phage sequences in (meta)-genomic sequences.
Language:Nextflow13 173 708
nf-core/variantcatalogue
Pipeline to generate variant catalogues, a list of variants and their frequencies in a population, from whole genome sequences.
Language:Nextflow13 178 16
nf-core/metapep
From metagenomes to epitopes and beyond
Language:Nextflow12 68 3210
nf-core/tbanalyzer
An nf-core (meta) pipeline for analysis of different members of Mycobacterium tuberculosis complex.
Language:Nextflow12 191 13
nf-core/hicar
Pipeline for HiCAR data, a robust and sensitive multi-omic co-assay for simultaneous measurement of transcriptome, chromatin accessibility and cis-regulatory chromatin contacts.
Language:Nextflow11 112 107
nf-core/datasync
nf-core/datasync is a system operation pipeline that provides several workflows for handling system operation / automation tasks
Language:Nextflow10 197 33
nf-core/phyloplace
nf-core/phyloplace is a bioinformatics best-practice analysis pipeline that performs phylogenetic placement with EPA-NG.
Language:Nextflow10 178 55
nf-core/pairgenomealign
Pairwise genome comparison pipeline using the LAST software to align a list of query genomes to a target genome, and plot the results
Language:Nextflow9 178 495
nf-core/rnadnavar
Pipeline for RNA and DNA integrated analysis for somatic mutation detection
Language:Nextflow8 158 89
nf-core/mitodetect
A-Z analysis of mitochondrial NGS data
Language:Nextflow71
nf-core/radseq
Variant-calling pipeline for Restriction site-associated DNA sequencing (RADseq).
Language:Nextflow7 183 45
nf-core/drop
Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders
Language:Nextflow5 203 183
nf-core/setup-nf-test
Language:JavaScript5 8 34
nf-core/testpipeline
A small example pipeline used to test new nf-core infrastructure and common code.
Language:Nextflow5 2 140
nf-core/spinningjenny
Pipeline for simulating the first industrial revolution using Agent Based Models.
Language:Nextflow4 159 14
nf-core/stableexpression
Pipeline dedicated to finding the most stable genes among a single or multiple expression dataset(s). It is useful in particular for finding the most suitable qPCR reference genes for a specific species.
Language:Nextflow4 1 01
nf-core/actions-runners
Instructions and scripts for custom GitHub Actions runners
Language:Shell3 6 14
nf-core/troughgraph
A quantitative assessment of the underlying permafrost landscapes and, per extension, of the level of permafrost thaw in the region
Language:Nextflow3 195 01
nf-core/evexplorer
Language:Nextflow11
nf-core/references-assets
Language:Shell1 1 01