Workflows

What is a Workflow?
834 Workflows visible to you, out of a total of 910
ONT-bacpac-nf
Stable

A rapid and portable workflow for pond-side sequencing of bacterial pathogens for sustainable aquaculture using ONT long-read sequencing.

Type: Nextflow

Creators: Georgina Samaha, Francisca Samsing, Mitchell O'Brien, Frederick Jaya

Submitter: Georgina Samaha

DOI: 10.48546/workflowhub.workflow.1263.1

nf-core/denovotranscript

GitHub Actions CI Status GitHub Actions Linting StatusAWS CI[![Cite ...

Type: Nextflow

Creator: Avani Bhojwani and Timothy Little

Submitter: WorkflowHub Bot

functional-annotation-protein-sequences/main

This workflow uses eggNOG mapper and InterProScan for functional annotation of protein sequences.

Type: Galaxy

Creators: Romane Libouban, Anthony Bretaudeau

Submitter: WorkflowHub Bot

Workflow for species distribution modeling with ModGP
Work-in-progress

Crop Wild Relatives distribution modeling workflow using the ModGP; a prototype Digital Twin from BioDT.

Type: Argo Workflow

Creator: Daniel Bauer

Submitter: Daniel Bauer

influenza-isolates-consensus-and-subtyping/main

This workflow performs subtyping and consensus sequence generation for batches of Illumina PE sequenced Influenza A isolates.

Type: Galaxy

Creators: Wolfgang Maier, Viktoria Isabel Schwarz

Submitter: WorkflowHub Bot

OMERO Nuclei Cell Counting, Image Import, Annotation and Region of Interests (ROIs) Workflow
Stable

Workflow to perform nuclei cell counting on High Content Screening (HCS) Data and upload result into OMERO

In this workflow, cell images are first uploaded to both Galaxy and OMERO using the “OMERO Image Import” tool. Concurrently, image processing is performed. After thresholding and binarization, key features of nuclei, such as area, label number, and perimeter, are computed from the processed images and saved as a CSV file. The result file is then attached to each image stored in OMERO using ...

Type: Galaxy

Creators: Riccardo Massei, Riccardo Massei

Submitter: Riccardo Massei

DOI: 10.48546/workflowhub.workflow.1259.1

OMERO Image Import, Annotation and Region of Interests (ROIs) Workflow
Stable

General workflow to upload data into OMERO using Galaxy

A dataset for testing can be found at: https://zenodo.org/records/14205500

Important Security Note: It is crucial to be aware that storing credentials as variables can pose security risks, particularly if accessed by administrators. Therefore, it is essential to handle user credentials securely and in accordance with best practices.

Type: Galaxy

Creators: Riccardo Massei, Matthias Bernt, Riccardo Massei

Submitter: Riccardo Massei

DOI: 10.48546/workflowhub.workflow.1258.1

OMERO Image Import and Annotation Workflow
Stable

General workflow to upload data into OMERO using KNIME

The workflow consists of two main branches: the Green Branch, which imports a folder containing images, and the Purple Branch, which enables the annotation of metadata as key-value pairs.

  • Fetching Images: The first step involves fetching images from a locally accessible folder.
  • User Authentication: Users are prompted to input their OMERO username and password through a Java snippet. This information is then converted into ...

Type: KNIME

Creator: Riccardo Massei

Submitter: Riccardo Massei

nf-core/nanostring

GitHub Actions CI Status GitHub Actions Linting StatusAWS CI[![Cite ...

Type: Nextflow

Creators: Peltzer , Alexander & Mohr, Christopher

Submitter: WorkflowHub Bot

scanpy-clustering/main

Single-cell RNA-seq workflow with Scanpy and Anndata. Based on the 3k PBMC clustering tutorial from Scanpy. It takes count matrix, barcodes and feature files as input and creates an Anndata object out of them. It then performs QC and filters for lowly expressed genes and cells. Then the data is normalized and scaled. Then PCs are computed to further cluster using louvain algorithm. It also generated various plots of clustering colored with highly ranked genes.

Type: Galaxy

Creators: Pavankumar Videm, Hans-Rudolf Hotz, Mehmet Tekman, Bérénice Batut

Submitter: WorkflowHub Bot

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