nf-core

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145 repositories

variantbenchmarking
Public
A nextflow variant benchmarking pipeline - premature
workflow benchmark pipeline nextflow draft variant-calling structural-variants nf-core
Nextflow
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MIT License
•7•12•15•0•Updated Nov 19, 2024Nov 19, 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•454•162•Updated Nov 19, 2024Nov 19, 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 19, 2024Nov 19, 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•34•Updated Nov 19, 2024Nov 19, 2024
oncoanalyser
Public
A comprehensive cancer DNA/RNA analysis and reporting pipeline
workflow pipeline nextflow nf-core
Nextflow
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MIT License
•8•50•13•3•Updated Nov 19, 2024Nov 19, 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
•274•88•11•15•Updated Nov 19, 2024Nov 19, 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•3•Updated Nov 18, 2024Nov 18, 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•254•33•Updated Nov 18, 2024Nov 18, 2024
sammyseq
Public
Pipeline for Sequential Analysis of MacroMolecules accessibilitY sequencing (SAMMY-seq) data, to analyze chromatin state.
workflow bioinformatics pipeline genomics genome nextflow ngs sequencing next-generation-sequencing dna
Nextflow
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MIT License
•3•1•3•1•Updated Nov 18, 2024Nov 18, 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
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MIT License
•42•62•16•0•Updated Nov 18, 2024Nov 18, 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
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MIT License
•30•18•15•8•Updated Nov 18, 2024Nov 18, 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•9•Updated Nov 18, 2024Nov 18, 2024
tfactivity
Public
Bioinformatics pipeline that makes use of expression and open chromatin data to identify differentially active transcription factors across conditions.
workflow transcription-factors pipeline nextflow transcriptomics nf-core open-chromatin-regions
Nextflow
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MIT License
•3•9•3•2•Updated Nov 18, 2024Nov 18, 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•409•261•33•Updated Nov 18, 2024Nov 18, 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 18, 2024Nov 18, 2024
phaseimpute
Public
A bioinformatics pipeline to phase and impute genetic data
pipeline genomics imputation genotype phasing low-pass-sequencing
Nextflow
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MIT License
•14•17•13•4•Updated Nov 18, 2024Nov 18, 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•1•Updated Nov 17, 2024Nov 17, 2024
epitopeprediction
Public
A bioinformatics best-practice analysis pipeline for epitope prediction and annotation
workflow nf-core epitope mhc-binding-prediction pipeline nextflow epitope-prediction
Nextflow
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MIT License
•22•42•14•1•Updated Nov 17, 2024Nov 17, 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 16, 2024Nov 16, 2024
references
Public
Nextflow
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MIT License
•3•3•8•0•Updated Nov 16, 2024Nov 16, 2024
setup-nf-test
Public
JavaScript
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MIT License
•2•2•0•0•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•64•59•6•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•88•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
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MIT License
•81•148•43•5•Updated Nov 15, 2024Nov 15, 2024
reportho
Public
nf-core pipeline for comparative analysis of ortholog predictions
Nextflow
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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•2•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