nextflow-pipeline
There are 88 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
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
mahesh-panchal/nf-cascade
A proof of concept daisy-chaining Nextflow workflows
cellgeni/cellatac
Sanger Cellular Genetics single-cell ATAC-seq pipeline.
INMEGEN/Pipelines_INMEGEN
Flujos de trabajos desarrollados y automatizados en el Inmegen para el procesamiento de datos genómicos y transcriptómicos.
AustralianBioCommons/Nextflow_DSL2_template
Template for creating Nextflow DSL2 pipelines
jhayer/baargin
Bacterial Assembly and Antimicrobial Resistance Genes In NextFlow
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
BirgitRijvers/EMC-MetaMicrobes
Nextflow pipeline to detect and classify microbial reads in sequencing data from human samples.
eipm/hello-mess-nf
A Nextflow pipeline to experiment with DSL2 + Zero Mess
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.
jeffe107/MAGFlow
Workflow for MAG quality assessment and taxonomical annotation.
mriffle/nf-skyline-dia-ms
Nextflow workflow for performing DIA proteomics
nschan/nf-genomeassembly
Nextflow pipeline to assemble genomes from long reads.
Sydney-Informatics-Hub/template-nf
A straightforward Nextflow workflow template generator.
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).
JLP-BioInf/rnaCrosslinkNF
Pre-processing pipeline for RNA crosslinking and High throughput sequencing data.
joanmarticarreras/VANIR
NextFlow pipeline for Virus Variant calling and de novo Assembly of Nanopore and Illumina Reads
bixBeta/nextflow
nextflow RNAseq pipeline for GG02
paq88/Variant_Calling_Nextflow_pipeline
Pipeline for SNP Calling Created in Nextflow management system for purposesof testing the advantages of managed systems vs native applications in variant calling. The paper created and published one day is titled "NextFlow vs. plain Bash: Different Approaches to the Parallelisation of SNP Calling from the Whole Genome Sequence Data"