Workflows

What is a Workflow?
837 Workflows visible to you, out of a total of 913
Work-in-progress

Digitial Twin Component for Earthquakes (DTC-E) WorkFlow 2 (WF7502) generates synthetic shaking simulations (shakemaps) for seismic sources at different time scales, and automatically incorporates new data as it becomes available.

The workflow consists of multiple steps (ST), datasets (DT), and software services (SS). Below is a simplified breakdown:

Data Ingestion & Preprocessing

  • ST750201: Assimilates real-time earthquake data from external sources.
  • ST750202: Extracts earthquake ...

Type: Common Workflow Language

Creators: Johannes Kemper, Cedric Bhihe, Georgina Díez

Submitter: Johannes Kemper

Decontamination Workflow

Decontamination (foreign contaminants and mitochondrial sequences) of genome assembly after scaffolding step. Part of the VGP Suite.

Inputs

  • Genome Assembly [fasta]
  • Database for Kraken2. Database containing the possible contaminants.

Ouput

  • List of contaminant scaffolds
  • List of mitochondrial scaffolds
  • Decontaminated assembly

Type: Galaxy

Creator: Nadolina Brajuka

Submitter: WorkflowHub Bot

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

Type: Nextflow

Creators: No author provided, Hadrien Gourlé, Daniel Straub, Sabrina Krakau

Submitter: WorkflowHub Bot

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

Type: Nextflow

Creators: Daniel Straub, Alexander Peltzer

Submitter: WorkflowHub Bot

Work-in-progress

AnnoAudit - Annotation Auditor

AnnoAudit is a robust Nextflow pipeline designed to evaluate the quality of genomic annotations through a multifaceted approach.

Overview of the workflow

The workflow assess the annotation quality based on different criteria:

  • Protein evidence support
  • RNASeq evidence support
  • Statistics of the predictions (i.e., gene length, exon number, etc.)
  • Ortholog analysis (BUSCO, OMArk)

Input data

  • Reference genome genome.[.fna, .fa, .fasta]
  • Annotation ...

Type: Nextflow

Creator: Phuong Doan

Submitter: Phuong Doan

DOI: 10.48546/workflowhub.workflow.1330.1

Stable

Prostate cancer classification workflow

This workflow segments tissue regions and classifies prostate cancer on H&E whole slide images, using AI. It consists of three steps:

  1. low-resolution tissue segmentation to select areas for further processing;

  2. high-resolution tissue segmentation to refine borders - it uses step 1 as input;

  3. high-resolution normal/cancer classification - it uses step 1 as input.

Type: Common Workflow Language

Creator: Mauro Del Rio

Submitter: Simone Leo

Stable

Tissue segmentation workflow

This workflow performs tissue segmentation on H&E whole slide images using AI.

Type: Common Workflow Language

Creator: Mauro Del Rio

Submitter: Simone Leo

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

Type: Nextflow

Creators: None

Submitter: WorkflowHub Bot

This workflow generates Hi-C contact maps for genome assemblies in the Pretext format. It is compatible with one or 2 haplotypes. It includes tracks for PacBio read coverage, Gaps, and telomeres. The Pretext files can be open in PretextView for the manual curation of genome assemblies.

Type: Galaxy

Creators: Patrik Smeds, Delphine Lariviere

Submitter: WorkflowHub Bot

Lysozyme in water full COMPSs application. Added new WRROC profile: Provenance Run Crate

Type: COMPSs

Creators: None

Submitter: Panna Lukacs

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