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nextflow-pipelines

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What_the_Phage

replikation /What_the_Phage

WtP: Phage identification via nextflow and docker or singularity

bioinformatics nextflow phages nextflow-pipelines phage-identification phage-sequences

UpdatedDec 5, 2025
Nextflow

Sydney-Informatics-Hub /Bioinformatics

A suite of bioinformatics data processing and analysis pipelines, software, and training resources for common methods.

bioinformatics snps genomics nextflow cancer somatic-variants ngs metagenomics bioinformatics-pipeline rnaseq variant-calling transcriptomics indels bioinformatics-analysis bioinformatics-scripts germline-variants research-computing nextflow-pipelines sydney-informatics-hub

UpdatedDec 12, 2025

Jianhua-Wang /GWAS-pipeline

From QC to summary statistics

gwas imputation association-analysis gwas-pipeline nextflow-pipelines

UpdatedJun 27, 2020
HTML

JaneliaSciComp /exllsm-circuit-reconstruction

Nextflow pipeline encapsulating workflows for analyzing expansion lattice light-sheet microscopy (ExLLSM) imagery

machine-learning pipeline image-processing neuroscience segmentation microscopy lightsheet nextflow-pipelines

UpdatedApr 10, 2025
Nextflow

angelovangel /nxf-fastqc

A simple fastp-MultiQC nextflow pipeline

multiqc fastq-files ngs-pipeline fastqc nextflow-pipelines

UpdatedFeb 2, 2023
Nextflow

CFSAN-Biostatistics /bettercallsal

Nextflow workflows to assign Salmonella serotype based on Genome similarity using MASH, SOURMASH and KMA.

nextflow metagenomics salmonella nextflow-pipelines ncbi-pathogens quasi-metagenomics

UpdatedOct 29, 2025
Nextflow

zqbake /hictools

Tools for processing HIC data.

hic nextflow-pipelines

UpdatedMay 21, 2021
Python

adamd3 /BactSeq

A nextflow pipeline for performing bacterial RNA-Seq data analysis.

pipeline nextflow bacteria nextflow-pipelines bacterial-genome-analysis

UpdatedOct 14, 2025
Nextflow

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.

nextflow docker-container docker-image recipe singularity singularity-containers nextflow-scif nextflow-pipelines scif-recipe nextflow-workflow

UpdatedFeb 25, 2019
HTML

Aveglia /vAMPirus

Automated virus amplicon sequencing analysis program integrated with Nextflow pipeline manager.

virus nextflow viruses amplicon amplicon-sequencing amplicon-pipeline nextflow-pipelines

UpdatedMay 23, 2024
Nextflow

elowy01 /vcf_filtering

Filter a VCF to discard false positive variants

machine-learning genomics variant-calling variant-filtration variant-analysis nextflow-pipelines

UpdatedNov 25, 2021
Python

JBris /nextflow-graph-machine-learning

A Nextflow pipeline demonstrating how to train graph neural networks for gene regulatory network reconstruction using DREAM5 data.

docker machine-learning deep-learning nextflow docker-compose minio variational-inference variational-autoencoder gene-regulatory-network graphsage graph-neural-networks mlops mlflow graph-neural-network nextflow-pipeline nextflow-pipelines gene-regulatory-networks gene-regulatory-network-inference dream5

UpdatedNov 20, 2024
Python

ifremer-bioinformatics /orson

Workflow for prOteome and tRanScriptome functiOnal aNnotation. CAUTION : project has moved to Gitlab.

workflow annotation proteome transcriptome nextflow-pipelines

UpdatedMar 3, 2023
Nextflow

igsr /igsr_analysis

This repo contains code that is relevant for the analysis (Mapping, BAM qc, Variant Calling, Filtering etc...) of IGSR data

python rna-seq perl jupyter-notebook pipelines snp-genotyping snp-data nextflow-pipelines

UpdatedDec 8, 2022
Jupyter Notebook

stracquadaniolab /apex-nf

APEX: Automated Protein EXpression in E. coli

nextflow lab-automation nextflow-pipelines opentrons opentrons-ot2

UpdatedJul 23, 2025
Python

dolphinnext /rnaseq

RNA-Seq pipeline

workflow rna-seq pipeline nextflow nextflow-pipelines

UpdatedMar 22, 2023
Nextflow

nschan /nf-genomeassembly

Nextflow pipeline to assemble genomes from long reads.

nanopore annotation genome nextflow pacbio scaffolding genome-sequencing oxford-nanopore genome-assembly long-reads arabidopsis hifi long-read-sequencing arabidopsis-thaliana nextflow-pipeline nextflow-pipelines pacbio-hifi-sequencing-reads

UpdatedMar 20, 2025
Nextflow

SCC-LZU /LGAflow

A Genome Annotation workflow for Eukaryotes

genome-annotation nextflow-pipelines

UpdatedMay 11, 2022
Nextflow

LieberInstitute /SPEAQeasyWorkshop2020

EuroBioc2020 SPEAQeasy workshophttps://eurobioc2020.bioconductor.org by Nick Eagles and Josh Stolz. For more information about SPEAQeasy checkhttp://research.libd.org/SPEAQeasy/. For an example on how to use this RNA-seq processing pipeline and analyze the output files checkhttp://research.libd.org/SPEAQeasy-example/.

nextflow rstats bioconductor limma nextflow-pipelines rnaseq-pipeline speaqeasy

UpdatedDec 10, 2024
R

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.

nextflow mlst subtyping nextflow-pipelines cronobacter ncbi-pathoges

UpdatedOct 3, 2025
Nextflow

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