nf-core

All

145 repositories

phaseimpute
Public
A bioinformatics pipeline to phase and impute genetic data
pipeline genomics imputation genotype phasing low-pass-sequencing
Nextflow
•
MIT License
•14•17•12•2•Updated Nov 24, 2024Nov 24, 2024
modules
Public
Repository to host tool-specific module files for the Nextflow DSL2 community!
modules nextflow pipelines workflows nf-core dsl2 nf-test
Nextflow
•
MIT License
•722•284•455•178•Updated Nov 24, 2024Nov 24, 2024
website
Public
Code and files for the main nf-core website.
website nextflow nf-core
MDX
•
MIT License
•196•69•91•34•Updated Nov 24, 2024Nov 24, 2024
spatialxe
Public
Nextflow
•
MIT License
•2•5•28•1•Updated Nov 23, 2024Nov 23, 2024
setup-nextflow
Public
A GitHub action to install Nextflow
nextflow actions
TypeScript
•
MIT License
•5•12•8•3•Updated Nov 23, 2024Nov 23, 2024
nascent
Public
Nascent Transcription Processing Pipeline
nextflow rna transcription tss gro-seq nf-core pro-seq nascent workflow pipeline
Nextflow
•
MIT License
•10•18•37•5•Updated Nov 23, 2024Nov 23, 2024
nanostring
Public
An analysis pipeline for Nanostring nCounter expression data.
workflow pipeline nextflow nanostring nanostringnorm nf-core
Nextflow
•
MIT License
•8•13•8•2•Updated Nov 22, 2024Nov 22, 2024
drugresponseeval
Public
Pipeline for testing drug response prediction models in a statistically and biologically sound way.
training workflow machine-learning bioinformatics deep-learning pipeline nextflow reproducible-research cross-validation drugs
Nextflow
•
MIT License
•1•4•4•1•Updated Nov 22, 2024Nov 22, 2024
fastquorum
Public
Pipeline to produce consensus reads using unique molecular indexes/barcodes (UMIs)
workflow pipeline nextflow consensus umi unique-molecular-identifier nf-core umis
Nextflow
•
MIT License
•10•20•14•2•Updated Nov 22, 2024Nov 22, 2024
test-datasets
Public
Test data to be used for automated testing with the nf-core pipelines
testing workflow nextflow test-data nf-core pipelines test-datasets
MIT License
•353•105•31•10•Updated Nov 22, 2024Nov 22, 2024
demultiplex
Public
Demultiplexing pipeline for sequencing data
nextflow illumina demultiplexing bcl2fastq nf-core bases2fastq elementbiosciences workflow pipeline
Nextflow
•
MIT License
•38•44•18•0•Updated Nov 22, 2024Nov 22, 2024
dualrnaseq
Public
Analysis of Dual RNA-seq data - an experimental method for interrogating host-pathogen interactions through simultaneous RNA-seq.
workflow rna-seq pipeline nextflow quantification nf-core host-pathogen dualrna-seq readmapping
Nextflow
•
MIT License
•30•18•15•8•Updated Nov 22, 2024Nov 22, 2024
coproid
Public
Coprolite host Identification pipeline
workflow microbiome adna nf-core ancient-dna coprolite pipeline nextflow
Nextflow
•
MIT License
•3•9•2•1•Updated Nov 22, 2024Nov 22, 2024
references
Public
Nextflow
•
MIT License
•4•4•9•1•Updated Nov 22, 2024Nov 22, 2024
bacass
Public
Simple bacterial assembly and annotation pipeline
workflow denovo genome-assembly denovo-assembly bacterial-genomes nanopore-sequencing nf-core nanopore pipeline nextflow
Nextflow
•
MIT License
•42•63•18•0•Updated Nov 22, 2024Nov 22, 2024
variantbenchmarking
Public
A nextflow variant benchmarking pipeline - premature
workflow benchmark pipeline nextflow draft variant-calling structural-variants nf-core
Nextflow
•
MIT License
•7•12•16•2•Updated Nov 22, 2024Nov 22, 2024
taxprofiler
Public
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
workflow bioinformatics nanopore pipeline nextflow shotgun pathogen metagenomics classification profiling
Nextflow
•
MIT License
•36•128•42•4•Updated Nov 22, 2024Nov 22, 2024
logos
Public
Host nf-core logos and templates for making new logos
nextflow logo nf-core
MIT License
•9•3•0•1•Updated Nov 22, 2024Nov 22, 2024
ops
Public
Python
•2•1•23•8•Updated Nov 22, 2024Nov 22, 2024
differentialabundance
Public
Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq
workflow rna-seq pipeline nextflow shiny deseq2 microarray chip-seq atac-seq differential-expression
Nextflow
•
MIT License
•37•64•58•4•Updated Nov 22, 2024Nov 22, 2024
configs
Public
Config files used to define parameters specific to compute environments at different Institutions
bioinformatics nextflow configuration pipelines workflows nf-core
Nextflow
•
MIT License
•275•88•12•15•Updated Nov 22, 2024Nov 22, 2024
nft-utils
Public
nf-test utility functions
Java
•
MIT License
•7•9•2•0•Updated Nov 22, 2024Nov 22, 2024
metapep
Public
From metagenomes to epitopes and beyond
workflow pipeline nextflow nf-core
Nextflow
•
MIT License
•5•8•13•1•Updated Nov 22, 2024Nov 22, 2024
raredisease
Public
Call and score variants from WGS/WES of rare disease patients.
workflow pipeline nextflow diagnostics variant-calling wgs snv wes variant-annotation structural-variants
Nextflow
•
MIT License
•34•90•32•0•Updated Nov 22, 2024Nov 22, 2024
mag
Public
Assembly and binning of metagenomes
workflow nanopore annotation nextflow metagenomics binning nanopore-sequencing nf-core long-read-sequencing bioinformatics
Nextflow
•
MIT License
•110•217•60•7•Updated Nov 22, 2024Nov 22, 2024
scrnaseq
Public
A single-cell RNAseq pipeline for 10X genomics data
workflow rna-seq pipeline nextflow single-cell kallisto 10x-genomics 10xgenomics nf-core bustools
Nextflow
•
MIT License
•172•214•53•4•Updated Nov 22, 2024Nov 22, 2024
pacvar
Public
Longread PacBio sequencing processing for WGS and PureTarget
alignment long-read pacbio variant-calling wgs puretarget
Nextflow
•
MIT License
•1•1•0•2•Updated Nov 21, 2024Nov 21, 2024
rnasplice
Public
rnasplice is a bioinformatics pipeline for RNA-seq alternative splicing analysis
workflow rna-seq pipeline nextflow alternative-splicing rna nf-core splicing
Nextflow
•
MIT License
•27•46•9•6•Updated Nov 21, 2024Nov 21, 2024
tools
Public
Python package with helper tools for the nf-core community.
bioinformatics linting linter nf-core python workflow pipeline nextflow
Python
•
MIT License
•191•242•258•36•Updated Nov 21, 2024Nov 21, 2024
ampliseq
Public
Amplicon sequencing analysis workflow using DADA2 and QIIME2
nextflow pacbio edna microbiome iontorrent illumina metabarcoding 16s rrna its
Nextflow
•
MIT License
•118•188•24•3•Updated Nov 21, 2024Nov 21, 2024