nextflow-pipeline
There are 99 repositories under nextflow-pipeline topic.
biocorecrg/master_of_pores
Nextflow pipeline for analysis of direct RNA Nanopore reads
Midnighter/nextflow-gotchas
A collection of unexpected challenges and learnings with nextflow and nf-core.
PalMuc/TransPi
TransPi – a comprehensive TRanscriptome ANalysiS PIpeline for de novo transcriptome assembly
bzhanglab/neoflow
NeoFlow: a proteogenomics pipeline for neoantigen discovery
mahesh-panchal/nf-cascade
A proof of concept daisy-chaining Nextflow workflows
nf-cmgg/structural
A bioinformatics best-practice analysis pipeline for calling structural variants (SVs), copy number variants (CNVs) and repeat region expansions (RREs) from short DNA reads
guigolab/geneidx
Nextflow pipeline for genome annotation of protein-coding genes
TORCH-Consortium/MAGMA
A pipeline for comprehensive genomic analyses of Mycobacterium tuberculosis with a focus on clinical decision making as well as research
cellgeni/cellatac
Sanger Cellular Genetics single-cell ATAC-seq pipeline.
DIncalciLab/samurai
A bioinformatics best-practice analysis pipeline for the analysis of shallow whole genome sequencing (sWGS) data for the identification of copy number alterations (CNAs).
INMEGEN/Pipelines_Inmegen
Flujos de trabajos desarrollados y automatizados en el Intituto Nacional de Medicina Genómica para el procesamiento de datos genómicos y transcriptómicos.
jhayer/baargin
Bacterial Assembly and Antimicrobial Resistance Genes In NextFlow
AustralianBioCommons/Nextflow_DSL2_template
Template for creating Nextflow DSL2 pipelines
jeffe107/MAGFlow
Workflow for MAG quality assessment and taxonomical annotation.
JBris/nextflow-graph-machine-learning
A Nextflow pipeline demonstrating how to train graph neural networks for gene regulatory network reconstruction using DREAM5 data.
kirilenkobm/py_nf
Python library to execute batches of jobs using nextflow.
angelovangel/nxf-bcl
A simple nextflow pipeline for Illumina run metrics (InterOp) and generation of fastq files (bcl2fastq)
BCCDC-PHL/dragonflye-nf
Nextflow wrapper for the dragonflye assembler, with additional QC
eipm/hello-mess-nf
A Nextflow pipeline to experiment with DSL2 + Zero Mess
ErasmusMC-Bioinformatics/EMC-MetaMicrobes
Nextflow pipeline to detect and classify microbial reads in sequencing data from human samples.
mriffle/nf-skyline-dia-ms
Nextflow workflow for performing DIA proteomics
phipsonlab/NextClone
Nextflow pipeline for extracting and counting clonal barcodes
salvadorlab/mbovpan
Mbovpan is a nextflow bioinformatic pipeline for Mycobacterium bovis pangenome analysis. The goal of Mbovpan is to help researchers to study the M. bovis pangenome in an automatic and easy way.
amchakra/tosca
Nextflow analysis pipeline for hiCLIP and proximity ligation sequencing data
asadprodhan/sangerFlow
A bioinformatics pipeline that automates the Sanger amplicon sequencing data analysis of thousands of samples in parallel.
bguo068/snp_call_nf
Nextflow pipeline for plasmodium SNP calling
biosustain/dsp_nf-metagenomics
Shotgun metagenomics pipeline to process microbiome samples
BU-ISCIII/panelLowFreq-nf
This is a nextflow pipeline for variant calling of low frequency variants in panel/WES high-throughput data.
nschan/nf-genomeassembly
Nextflow pipeline to assemble genomes from long reads.
renatosantos98/ont-benchmark
Supporting data for the publication "Investigating the performance of Oxford Nanopore long-read sequencing with respect to Illumina microarrays and short-read sequencing"
Sydney-Informatics-Hub/template-nf
A straightforward Nextflow workflow template generator.
JLP-BioInf/rnaCrosslinkNF
Pre-processing pipeline for RNA crosslinking and High throughput sequencing data.
vonMeyennLab/nf_cutntag
A Nextflow pipeline to perform quality control, alignment, and feature coverage of CUT&Tag sequencing data.