nf-core

All

152 repositories

modules
Public
Repository to host tool-specific module files for the Nextflow DSL2 community!
modules nextflow pipelines workflows nf-core dsl2 nf-test
Nextflow
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MIT License
•749•291•460•188•Updated Feb 2, 2025Feb 2, 2025
website
Public
Code and files for the main nf-core website.
website nextflow nf-core
MDX
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MIT License
•209•69•90•35•Updated Feb 2, 2025Feb 2, 2025
ops
Public
Python
•2•1•36•10•Updated Feb 2, 2025Feb 2, 2025
fastqrepair
Public
A pipeline that can be used to recover corrupted FASTQ.gz files, drop or fix uncompliant reads, remove unpaired reads, and settles reads that became disordered
corruption fastq-format fastq data-cleaning data-recovery well-formed recovery-tool fastq-corrupted unpaired-reads reads-interleaving
Nextflow
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MIT License
•2•2•5•1•Updated Feb 1, 2025Feb 1, 2025
metatdenovo
Public
Assembly and annotation of metatranscriptomic or metagenomic data for prokaryotic, eukaryotic and viruses.
workflow pipeline nextflow metagenomics viruses metatranscriptomics prokaryotes eukaryotes nf-core
Nextflow
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MIT License
•11•23•13•1•Updated Feb 1, 2025Feb 1, 2025
pairgenomealign
Public
Pairwise genome comparison pipeline using the LAST software to align a list of query genomes to a target genome, and plot the results
bioinformatics genomics nextflow comparative-genomics synteny last pairwise-alignment whole-genome-alignment nf-core dot-plot
Nextflow
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MIT License
•3•6•13•1•Updated Feb 1, 2025Feb 1, 2025
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
•193•246•275•40•Updated Feb 1, 2025Feb 1, 2025
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
•2•3•1•3•Updated Jan 31, 2025Jan 31, 2025
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
•37•93•34•2•Updated Jan 31, 2025Jan 31, 2025
setup-nextflow
Public
A GitHub action to install Nextflow
nextflow actions
TypeScript
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MIT License
•6•14•8•5•Updated Jan 31, 2025Jan 31, 2025
logos
Public
Host nf-core logos and templates for making new logos
nextflow logo nf-core
MIT License
•10•4•0•0•Updated Jan 31, 2025Jan 31, 2025
funcscan
Public
(Meta-)genome screening for functional and natural product gene sequences
workflow bioinformatics pipeline nextflow amp assembly function metagenomics amr screening
Nextflow
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MIT License
•22•78•16•3•Updated Jan 31, 2025Jan 31, 2025
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
•366•114•31•19•Updated Jan 31, 2025Jan 31, 2025
spatialxe
Public
Nextflow
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MIT License
•3•7•33•0•Updated Jan 31, 2025Jan 31, 2025
riboseq
Public
Pipeline for the analysis of ribosome profiling, or Ribo-seq (also named ribosome footprinting) data.
workflow pipeline nextflow nf-core
Nextflow
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MIT License
•8•12•14•1•Updated Jan 31, 2025Jan 31, 2025
proteinfamilies
Public
Generation and update of protein families
workflow bioinformatics pipeline nextflow metagenomics proteomics protein-families nf-core
Nextflow
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MIT License
•1•2•0•1•Updated Jan 31, 2025Jan 31, 2025
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
•9•14•13•2•Updated Jan 31, 2025Jan 31, 2025
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
•6•1•1•0•Updated Jan 31, 2025Jan 31, 2025
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
•42•72•78•6•Updated Jan 31, 2025Jan 31, 2025
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
•23•43•19•2•Updated Jan 31, 2025Jan 31, 2025
mag
Public
Assembly and binning of metagenomes
workflow nanopore annotation nextflow metagenomics binning nanopore-sequencing nf-core long-read-sequencing bioinformatics
Nextflow
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MIT License
•116•226•59•13•Updated Jan 31, 2025Jan 31, 2025
createtaxdb
Public
Parallelised and automated construction of metagenomic classifier databases of different tools
workflow database pipeline nextflow metagenomics profiling nf-core database-builder taxonomic-profiling metagenomic-profiling
Nextflow
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MIT License
•7•8•13•2•Updated Jan 31, 2025Jan 31, 2025
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
•2•6•3•0•Updated Jan 31, 2025Jan 31, 2025
methylong
Public
Extract methylation calls from long reads (ONT/ PacBio)
1•1•0•1•Updated Jan 31, 2025Jan 31, 2025
magmap
Public
Nextflow
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MIT License
•4•4•11•1•Updated Jan 31, 2025Jan 31, 2025
troughgraph
Public
A quantitative assessment of the underlying permafrost landscapes and, per extension, of the level of permafrost thaw in the region
Nextflow
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MIT License
•1•2•0•0•Updated Jan 31, 2025Jan 31, 2025
rnaseq
Public
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
workflow rna-seq pipeline nextflow rna nf-core
Nextflow
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MIT License
•717•973•68•11•Updated Jan 31, 2025Jan 31, 2025
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
•285•93•12•17•Updated Jan 31, 2025Jan 31, 2025
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
•82•158•38•8•Updated Jan 31, 2025Jan 31, 2025
references-assets
Public
Shell
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MIT License
•1•0•0•0•Updated Jan 31, 2025Jan 31, 2025