nextflow-pipelines
There are 44 repositories under nextflow-pipelines topic.
replikation/What_the_Phage
WtP: Phage identification via nextflow and docker or singularity
Jianhua-Wang/GWAS-pipeline
From QC to summary statistics
JaneliaSciComp/exllsm-circuit-reconstruction
Nextflow pipeline encapsulating workflows for analyzing expansion lattice light-sheet microscopy (ExLLSM) imagery
Sydney-Informatics-Hub/Bioinformatics
A suite of bioinformatics data processing and analysis pipelines, software, and training resources for common methods.
angelovangel/nxf-fastqc
A simple fastp-MultiQC nextflow pipeline
zhqu1148980644/hictools
Tools for processing HIC data.
Aveglia/vAMPirus
Automated virus amplicon sequencing analysis program integrated with Nextflow pipeline manager.
BU-ISCIII/nextflow-scif
This is a demo about how to develop and deploy a pipeline using nextflow, scif, a container (Singularity and Docker) and its posterior deployment.
CFSAN-Biostatistics/bettercallsal
Nextflow workflows to assign Salmonella serotype based on Genome similarity using MASH, SOURMASH and KMA.
adamd3/BactSeq
A nextflow pipeline for performing bacterial RNA-Seq data analysis.
elowy01/vcf_filtering
Filter a VCF to discard false positive variants
ifremer-bioinformatics/orson
Workflow for prOteome and tRanScriptome functiOnal aNnotation. CAUTION : project has moved to Gitlab.
JBris/nextflow-graph-machine-learning
A Nextflow pipeline demonstrating how to train graph neural networks for gene regulatory network reconstruction using DREAM5 data.
igsr/igsr_analysis
This repo contains code that is relevant for the analysis (Mapping, BAM qc, Variant Calling, Filtering etc...) of IGSR data
CFSAN-Biostatistics/cronology
cronology is an automated workflow for Cronobacter whole genome sequence assembly, subtyping and isolate clustering based on NCBI Pathogen Detection Project for Cronobacter.
dolphinnext/rnaseq
RNA-Seq pipeline
LieberInstitute/SPEAQeasyWorkshop2020
EuroBioc2020 SPEAQeasy workshop https://eurobioc2020.bioconductor.org by Nick Eagles and Josh Stolz. For more information about SPEAQeasy check http://research.libd.org/SPEAQeasy/. For an example on how to use this RNA-seq processing pipeline and analyze the output files check http://research.libd.org/SPEAQeasy-example/.
angelovangel/nxf-dada2
A nextflow pipeline for the analysis of 16S amplicon data built around RExMap
azavea/pipeline-playground
A repository with usage examples of various pipeline and workflow orchestration tools
biodata-fun/nf_genomics_pipelines
This repo contains pipeline implemented using the nextflow workflow management system for the analysis of genomics data
cobinet/HLA_lli
HLA typing pipelines in nextflow
GaitiLab/nf-processes
modules for processing and analyzing single cell data using Nextflow
stracquadaniolab/apex-nf
APEX: Automated Protein EXpression in E. coli
adamd3/OrthoQuant
A Nextflow pipeline for performing bacterial RNA-Seq analysis without a reference genome.
biodata-fun/course_material
This directory contains material that I've used in different courses
dolphinnext/atacseq
Atac-Seq pipeline
dolphinnext/chipseq
Chip-Seq pipeline
JBris/nextflow-tutorials
Working through NextFlow tutorials. See https://github.com/nextflow-io/training
lgi-onehealth/ref-match-db
A nextflow workflow to build referenceseeker DBs on the fly
nschan/nf-arassembly
Nextflow pipeline to assemble genomes from nanopore reads.
SCC-LZU/LGAflow
A Genome Annotation workflow for Eukaryotes
rajanbit/Bioinfo_nf_Scripts
Nextflow Scripts/Workflows for Bioinformatics
TheSergeyPixel/nf_target
Nextflow pipeline for targeted sequencing data.
asadprodhan/phyloTree
Bayesian phylogenetic analysis
Open-Science-Community-Saudi-Arabia/moleculardymics
This workflow for molecular dynamics simulation of proteins