Workflows

What is a Workflow?
1308 Workflows visible to you, out of a total of 1393
Stable

The workflow takes trimmed HiC paired-end reads collection, and Pri/Alt assemblies to produce a scaffolded primary assembly (and alternate contigs) using YaHS. It also runs Pretext and all the QC analyses (gfastats, BUSCO, and Merqury).

Type: Galaxy

Creators: Diego De Panis, ERGA

Submitter: Diego De Panis

Stable

The workflow takes a long reads collection (HiFi, or ONT also possible now), and max coverage depth (calculated from WF1) to run Hifiasm in solo mode. It produces a Pri/Alt assembly, Bandage plots, and runs all the QC analysis (gfastats, BUSCO, and Merqury).

Type: Galaxy

Creators: Diego De Panis, ERGA

Submitter: Diego De Panis

DOI: 10.48546/workflowhub.workflow.1162.1

SeuratExtend: An Enhanced Toolkit for scRNA-seq Analysis

Overview

SeuratExtend is an R package designed to provide an improved and easy-to-use toolkit for scRNA-seq analysis and visualization, built upon the Seurat object. While Seurat is a widely-used tool in the R community that offers a foundational framework for scRNA-seq analysis, it has limitations when it comes to more advanced analysis and customized visualization. SeuratExtend expands upon Seurat by offering an array of ...

Type: Unrecognized workflow type

Creator: Yichao Hua

Submitter: Yichao Hua

DOI: 10.48546/workflowhub.workflow.1385.1

Application that perform the multiplication between matrices.

Type: COMPSs

Creator: Raül Sirvent

Submitter: Nicolò Giacomini

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

Type: Nextflow

Creators: Luisa Santus, Jose Espinosa Carrasco

Submitter: WorkflowHub Bot

This workflow is composed with the XCMS tool R package (Smith, C.A. 2006) able to extract, filter, align and fill gapand the possibility to annotate isotopes, adducts and fragments using the CAMERA R package (Kuhl, C 2012).

https://training.galaxyproject.org/training-material/topics/metabolomics/tutorials/lcms-preprocessing/tutorial.html

Type: Galaxy

Creator: workflow4metabolomics

Submitter: WorkflowHub Bot

K-means COMPSs application

Type: COMPSs

Creator: Rosa M Badia

Submitter: Panna Lukacs

Stable

Gene_fetch

This tool fetches gene sequences from NCBI databases based on taxonomy IDs (taxids) or taxonomic information. It can retrieve both protein and nucleotide sequences for various genes, including protein-coding genes (e.g., cox1, cytb, rbcl, matk) and rRNA genes (e.g., 16S, 18S).

Feature highlight

  • Fetch protein and/or nucleotide sequences from NCBI GenBank database.
  • Handles both direct nucleotide sequences and protein-linked nucleotide searches (CDS extraction includes fallback ...

Type: Python

Creators: Dan Parsons, Ben Price

Submitter: Dan Parsons

Work-in-progress

Annual percentage Change for population in Germany (1950 - 2025)

This workflow run was executed on Galaxy (Workflow Rerun Information)

Workflow: Climate Stripes

Execution Status: scheduled

Executed: 2025-05-27 14:14:07.240149

Workflow Inputs

Formal Input Definitions

  • Germany-Population-Annual--Change-2025-05-27-15-17.csv (File)

  • Column name to use for plotting (Text)

  • Plot Title (Text)

  • nxsplit (Integer)

  • Description: Number of values per intervals

...

Work-in-progress

EOSC4Cancer_D2.2

Galaxy workflow used for EOSC4Cancer D2.2 - Analytical methods for data extraction, processing and sharing using biomedical images - demonstrator

Link to deliverable report on Zenodo:

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