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Search results for nextflow
nextflow
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362 search results found
Nextflow
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2,447
A DSL for data-driven computational pipelines
Rnaseq
⭐
718
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
Awesome Nextflow
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448
A curated list of nextflow based pipelines
Patterns
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316
A curated collection of Nextflow implementation patterns
Sarek
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299
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
Bactopia
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281
A flexible pipeline for complete analysis of bacterial genomes
Flowcraft
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234
FlowCraft: a component-based pipeline composer for omics analysis using Nextflow. 🐳📦
Tools
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205
Python package with helper tools for the nf-core community.
Modules
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180
Repository to host tool-specific module files for the Nextflow DSL2 community!
Npm Groovy Lint
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172
Lint, format and auto-fix your Groovy / Jenkinsfile / Gradle files using command line
Mag
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164
Assembly and binning of metagenomes
Atacseq
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145
ATAC-seq peak-calling and QC analysis pipeline
Chipseq
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144
ChIP-seq peak-calling, QC and differential analysis pipeline.
Ampliseq
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141
Amplicon sequencing analysis workflow using DADA2 and QIIME2
Sarek
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126
Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing
Nf Tower
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122
Nextflow Tower system
Nanoseq
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122
Nanopore demultiplexing, QC and alignment pipeline
Methylseq
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121
Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
Rnafusion
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120
RNA-seq analysis pipeline for detection gene-fusions
Scrnaseq
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119
A single-cell RNAseq pipeline for 10X genomics data
Dockstore
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113
Our VM/Docker sharing infrastructure and management component
Eager
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112
A fully reproducible and state-of-the-art ancient DNA analysis pipeline
Nf Test
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102
Simple test framework for Nextflow pipelines
Viralrecon
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101
Assembly and intrahost/low-frequency variant calling for viral samples
Emg Viral Pipeline
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98
VIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies
What_the_phage
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96
WtP: Phage identification via nextflow and docker or singularity
Fetchngs
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93
Pipeline to fetch metadata and raw FastQ files from public and private databases
Dolphinnext
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92
A graphical user interface for distributed data processing of high throughput genomics
Mcmicro
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92
Multiple-choice microscopy pipeline
H3agwas
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89
GWAS Pipeline for H3Africa
Nextflow Demos
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88
Example Nextflow pipelines and programming techniques
Bacannot
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85
Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.
Ncov2019 Artic Nf
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85
A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformat with a focus on ncov2019
Training
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82
Nextflow training material
Pgsc_calc
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81
The Polygenic Score Catalog Calculator is a nextflow pipeline for polygenic score calculation
Test Datasets
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81
Test data to be used for automated testing with the nf-core pipelines
Distiller Nf
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80
A modular Hi-C mapping pipeline
Taxprofiler
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78
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
Master_of_pores
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77
Nextflow pipeline for analysis of direct RNA Nanopore reads
Callings Nf
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76
GATK RNA-Seq Variant Calling in Nextflow
Configs
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73
Config files used to define parameters specific to compute environments at different Institutions
Lncpipe
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71
Wf Human Variation
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67
Vsn Pipelines
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65
A repository of pipelines for single-cell data in Nextflow DSL2
Vscode Groovy Lint
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65
VSCode extension to lint , correct and format groovy and Jenkinsfile
Raredisease
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64
Call and score variants from WGS/WES of rare disease patients.
Smrnaseq
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63
A small-RNA sequencing analysis pipeline
Hic
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63
Analysis of Chromosome Conformation Capture data (Hi-C)
Rnaseq Nf
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59
A proof of concept of RNAseq pipeline
Nanoclust
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59
NanoCLUST is an analysis pipeline for UMAP-based classification of amplicon-based full-length 16S rRNA nanopore reads
Website
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58
Code and files for the main nf-core website.
Metontiime
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57
A Meta-barcoding pipeline for analysing ONT data in QIIME2 framework
Muffin
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56
hybrid assembly and differential binning workflow for metagenomics, transcriptomics and pathway analysis
Nextneopi
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55
nextNEOpi: a comprehensive pipeline for computational neoantigen prediction
Cutandrun
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54
Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes QC, support for spike-ins, IgG controls, peak calling and downstream analysis.
Nf Gwas
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52
A nextflow pipeline to perform state-of-the-art genome-wide association studies.
Pytest Workflow
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52
Configure workflow/pipeline tests using yaml files.
Yamp
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52
YAMP: Yet Another Metagenomic Pipeline
Mpgap
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51
Multi-platform genome assembly pipeline for Illumina, Nanopore and PacBio reads
Rare Disease Wf
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49
(WIP) best-practices workflow for rare disease
Ngi Rnaseq
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49
Nextflow RNA-Seq Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.
Funcscan
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49
(Meta-)genome screening for functional and natural product gene sequences
Nextflowsnippets
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48
This repository hosts a large collection of Nextflow snippets
Bacass
⭐
47
Simple bacterial assembly and annotation pipeline
Nextflow.py
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46
Python wrapper around Nextflow.
Bactmap
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45
A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences
Easyfuse
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44
EasyFuse is a pipeline for accurate fusion gene detection from RNA-seq data.
Tractoflow
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44
TractoFlow: A robust, efficient and reproducible diffusion MRI pipeline leveraging Nextflow & Singularity
Nextflow_cheatsheet
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42
Tips for Nextflow and cheatsheet for channel operation
Covviz
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42
Multi-sample genome coverage viewer to observe large, coverage-based anomalies alongside annotations and sample metadata
Pipelines Nextflow
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41
A set of workflows written in Nextflow for Genome Annotation.
Airrflow
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40
B-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framework
Needlestack
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39
Multi-sample somatic variant caller
Aws For Bioinformatics
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38
AWS for Bioinformatics Researchers
Nf Validation
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38
Params validation plugin for Nextflow pipelines
Porecov
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38
SARS-CoV-2 workflow for nanopore sequence data
Deepvariant
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38
Google's DeepVariant variant caller as a Nextflow pipeline
Nf Shard
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36
Nextflow runs monitoring and organisation UI
Cecret
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36
Reference-based consensus creation
Iarc Nf
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35
List of IARC bioinformatics nextflow pipelines
Hifi 16s Workflow
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35
Nextflow pipeline to analyze PacBio HiFi full-length 16S data
Grape Nf
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35
An automated RNA-seq pipeline using Nextflow
Wf Metagenomics
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34
Metagenomic classification of long-read sequencing data
Hlatyping
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34
Precision HLA typing from next-generation sequencing data
Spatialtranscriptomics
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34
Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.
Differentialabundance
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34
Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq
Proteomicslfq
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32
Proteomics label-free quantification (LFQ) analysis pipeline
Circrna
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32
circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data
Openproblems V2
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31
Formalizing and benchmarking open problems in single-cell genomics
Nf Hack17 Tutorial
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31
Nextflow basic tutorial for newbie users
Rnadeseq
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31
Differential gene expression analysis and pathway analysis of RNAseq data
Demultiplex
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31
Demultiplexing pipeline for sequencing data
Nextflow Gotchas
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29
A collection of unexpected challenges and learnings with nextflow and nf-core.
Epitopeprediction
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28
A bioinformatics best-practice analysis pipeline for epitope prediction and annotation
Aradeepopsis
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28
A versatile, fully open-source pipeline to extract phenotypic measurements from plant images
Multifish
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28
EASI-FISH analysis pipeline for spatial transcriptomics
Mhcquant
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28
Identify and quantify MHC eluted peptides from mass spectrometry raw data
Camitax
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28
CAMITAX: Taxon labels for microbial genomes
Pangenome
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28
Renders a collection of sequences into a pangenome graph.
Gemmaker
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26
A workflow for construction of Gene Expression count Matrices (GEMs). Useful for Differential Gene Expression (DGE) analysis and Gene Co-Expression Network (GCN) construction
Related Searches
Pipeline Nextflow (284)
Nextflow Nf Core (75)
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Docker Nextflow (58)
Sequencing Nextflow (33)
Fastq Nextflow (31)
Python Nextflow (30)
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