nf-core

All

145 repositories

configs
Public
Config files used to define parameters specific to compute environments at different Institutions
bioinformatics nextflow configuration pipelines workflows nf-core
Nextflow
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MIT License
•273•88•11•15•Updated Nov 16, 2024Nov 16, 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
•719•283•450•158•Updated Nov 16, 2024Nov 16, 2024
website
Public
Code and files for the main nf-core website.
website nextflow nf-core
MDX
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MIT License
•196•69•89•35•Updated Nov 16, 2024Nov 16, 2024
sarek
Public
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
bioinformatics annotation genomics nextflow cancer reproducible-research containers conda next-generation-sequencing variant-calling
Nextflow
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MIT License
•415•408•261•35•Updated Nov 15, 2024Nov 15, 2024
nanostring
Public
An analysis pipeline for Nanostring nCounter expression data.
workflow pipeline nextflow nanostring nanostringnorm nf-core
Nextflow
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MIT License
•8•13•13•2•Updated Nov 15, 2024Nov 15, 2024
setup-nextflow
Public
A GitHub action to install Nextflow
nextflow actions
TypeScript
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MIT License
•5•12•8•3•Updated Nov 15, 2024Nov 15, 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
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MIT License
•10•20•14•2•Updated Nov 15, 2024Nov 15, 2024
setup-nf-test
Public
JavaScript
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MIT License
•2•2•0•0•Updated Nov 15, 2024Nov 15, 2024
tools
Public
Python package with helper tools for the nf-core community.
bioinformatics linting linter nf-core python workflow pipeline nextflow
Python
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MIT License
•191•242•252•33•Updated Nov 15, 2024Nov 15, 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
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MIT License
•1•4•4•1•Updated Nov 15, 2024Nov 15, 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
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MIT License
•37•63•58•5•Updated Nov 15, 2024Nov 15, 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
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MIT License
•34•87•32•0•Updated Nov 15, 2024Nov 15, 2024
ops
Public
Python
•2•1•23•8•Updated Nov 15, 2024Nov 15, 2024
coproid
Public
Coprolite host Identification pipeline
workflow microbiome adna nf-core ancient-dna coprolite pipeline nextflow
Nextflow
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MIT License
•2•9•2•1•Updated Nov 15, 2024Nov 15, 2024
spatialvi
Public
Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.
workflow bioinformatics rna-seq pipeline nextflow image-processing spatial transcriptomics single-cell microscopy
Nextflow
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MIT License
•19•52•5•0•Updated Nov 15, 2024Nov 15, 2024
eager
Public
A fully reproducible and state-of-the-art ancient DNA analysis pipeline
workflow metagenomics population-genetics adna pathogen-genomics nf-core ancientdna bioinformatics pipeline genome
Nextflow
•
MIT License
•81•148•43•5•Updated Nov 15, 2024Nov 15, 2024
reportho
Public
nf-core pipeline for comparative analysis of ortholog predictions
Nextflow
•
MIT License
•4•9•5•0•Updated Nov 15, 2024Nov 15, 2024
pacvar
Public
Longread PacBio sequencing processing for WGS and PureTarget
alignment long-read pacbio variant-calling wgs puretarget
Nextflow
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MIT License
•1•1•0•1•Updated Nov 15, 2024Nov 15, 2024
proteinfold
Public
Protein 3D structure prediction pipeline
nextflow protein-structure protein-sequences protein-folding protein-fold-prediction nf-core alphafold2 workflow pipeline
Nextflow
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MIT License
•38•58•24•2•Updated Nov 15, 2024Nov 15, 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
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MIT License
•172•214•52•5•Updated Nov 15, 2024Nov 15, 2024
ampliseq
Public
Amplicon sequencing analysis workflow using DADA2 and QIIME2
nextflow pacbio edna microbiome iontorrent illumina metabarcoding 16s rrna its
Nextflow
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MIT License
•117•187•25•2•Updated Nov 15, 2024Nov 15, 2024
rnavar
Public
gatk4 RNA variant calling pipeline
workflow pipeline nextflow rnaseq rna variant-calling nf-core gatk4 worflow
Nextflow
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MIT License
•32•37•39•3•Updated Nov 15, 2024Nov 15, 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 15, 2024Nov 15, 2024
methylseq
Public
Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
workflow pipeline nextflow dna-methylation rrbs methyl-seq epigenomics bisulfite-sequencing nf-core epigenome
Nextflow
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MIT License
•145•140•31•6•Updated Nov 15, 2024Nov 15, 2024
nascent
Public
Nascent Transcription Processing Pipeline
nextflow rna transcription tss gro-seq nf-core pro-seq nascent workflow pipeline
Nextflow
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MIT License
•10•18•37•4•Updated Nov 15, 2024Nov 15, 2024
oncoanalyser
Public
A comprehensive cancer DNA/RNA analysis and reporting pipeline
workflow pipeline nextflow nf-core
Nextflow
•
MIT License
•8•49•13•3•Updated Nov 14, 2024Nov 14, 2024
seqinspector
Public
QC pipeline to inspect your sequences
workflow quality-control pipeline genomics nextflow nf-core
Nextflow
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MIT License
•21•6•28•8•Updated Nov 14, 2024Nov 14, 2024
rnafusion
Public
RNA-seq analysis pipeline for detection of gene-fusions
workflow rna-seq pipeline nextflow gene-fusion fusion rna fusion-genes nf-core
Nextflow
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MIT License
•94•143•24•4•Updated Nov 14, 2024Nov 14, 2024
metapep
Public
From metagenomes to epitopes and beyond
workflow pipeline nextflow nf-core
Nextflow
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MIT License
•5•8•13•2•Updated Nov 13, 2024Nov 13, 2024
scdownstream
Public
A single cell transcriptomics pipeline for QC, integration and making the data presentable
quality-control integration clustering dimensionality-reduction single-cell scverse
Nextflow
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MIT License
•12•40•26•2•Updated Nov 13, 2024Nov 13, 2024