nf-core

All

143 repositories

setup-nextflow
Public
A GitHub action to install Nextflow
nextflow actions
TypeScript
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MIT License
•4•12•8•3•Updated Nov 2, 2024Nov 2, 2024
website
Public
Code and files for the main nf-core website.
website nextflow nf-core
MDX
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MIT License
•193•68•89•34•Updated Nov 2, 2024Nov 2, 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
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MIT License
•714•280•447•165•Updated Nov 2, 2024Nov 2, 2024
ops
Public
Python
•2•1•23•9•Updated Nov 2, 2024Nov 2, 2024
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
•1•0•3•1•Updated Nov 1, 2024Nov 1, 2024
modules-template
Public
0•0•0•0•Updated Nov 1, 2024Nov 1, 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•86•34•0•Updated Nov 1, 2024Nov 1, 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
•272•87•11•11•Updated Nov 1, 2024Nov 1, 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
•
MIT License
•144•140•28•5•Updated Nov 1, 2024Nov 1, 2024
oncoanalyser
Public
A comprehensive cancer DNA/RNA analysis and reporting pipeline
workflow pipeline nextflow nf-core
Nextflow
•
MIT License
•8•43•13•2•Updated Oct 31, 2024Oct 31, 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
•9•20•12•2•Updated Oct 31, 2024Oct 31, 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
•190•241•250•35•Updated Oct 31, 2024Oct 31, 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
•351•105•31•9•Updated Oct 31, 2024Oct 31, 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
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MIT License
•34•128•42•6•Updated Oct 31, 2024Oct 31, 2024
demultiplex
Public
Demultiplexing pipeline for sequencing data
nextflow illumina demultiplexing bcl2fastq nf-core bases2fastq elementbiosciences workflow pipeline
Nextflow
•
MIT License
•37•44•18•0•Updated Oct 31, 2024Oct 31, 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
•0•4•4•1•Updated Oct 31, 2024Oct 31, 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 Oct 31, 2024Oct 31, 2024
denovotranscript
Public
A pipeline for de novo transcriptome assembly of paired-end short reads from bulk RNA-seq
rna-seq transcriptome denovo-assembly
Nextflow
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MIT License
•2•3•3•1•Updated Oct 31, 2024Oct 31, 2024
pathogensurveillance
Public
Surveillance of pathogens using population genomics and sequencing
workflow pipeline nextflow nf-core
HTML
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MIT License
•5•12•37•0•Updated Oct 30, 2024Oct 30, 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•16•13•2•Updated Oct 30, 2024Oct 30, 2024
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
•6•8•14•2•Updated Oct 30, 2024Oct 30, 2024
mhcquant
Public
Identify and quantify MHC eluted peptides from mass spectrometry raw data
workflow pipeline nextflow dda mhc mass-spectrometry openms peptides nf-core immunopeptidomics
Nextflow
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MIT License
•25•33•10•0•Updated Oct 30, 2024Oct 30, 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
•36•61•53•9•Updated Oct 30, 2024Oct 30, 2024
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
•20•74•15•1•Updated Oct 30, 2024Oct 30, 2024
nft-tiff
Public
A plugin to make testing of tiff files much simpler
Java
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MIT License
•2•0•0•0•Updated Oct 30, 2024Oct 30, 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
•169•211•55•4•Updated Oct 30, 2024Oct 30, 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•37•28•1•Updated Oct 30, 2024Oct 30, 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•5•28•10•Updated Oct 30, 2024Oct 30, 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
•407•404•259•32•Updated Oct 30, 2024Oct 30, 2024
tbanalyzer
Public
An nf-core (meta) pipeline for analysis of different members of Mycobacterium tuberculosis complex.
workflow pipeline nextflow reproducible-research mycobacterium-tuberculosis-complex nf-core mycobacterium-tuberculosis
Nextflow
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MIT License
•1•7•1•1•Updated Oct 30, 2024Oct 30, 2024