Workflows

What is a Workflow?
816 Workflows visible to you, out of a total of 890
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 perform the scaffolding of a genome assemble using HiC data with YAHS. Part of the VGP set of workflows.

Type: Galaxy

Creator: VGP, Galaxy

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

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

Type: Nextflow

Creators: None

Submitter: WorkflowHub Bot

Genome Assembly with Hifi reads and Trio Data

Generate phased assembly based on PacBio Hifi Reads using parental Illumina data for phasing. Part of the VGP workflow suite, it needs to be run after the Trio k-mer Profiling workflow VGP2.

Inputs

  1. Hifi long reads [fastq]
  2. Concatenated Illumina reads : Paternal [fastq]
  3. Concatenated Illumina reads : Maternal [fastq]
  4. K-mer database [meryldb] generated by VGP2 workflow.
  5. Paternal hapmer database [meryldb] generated by VGP2 workflow.

...

Type: Galaxy

Creator: Galaxy, VGP

Submitter: WorkflowHub Bot

Purge contigs marked as duplicates by purge_dups (could be haplotypic duplication or overlap duplication). This workflow is the 6th workflow of the VGP pipeline. It is meant to be run after one of the contigging steps (Workflow 3, 4, or 5)

Type: Galaxy

Creator: Galaxy, VGP

Submitter: WorkflowHub Bot

Purge duplicates from one haplotype. Prerequisites: run after a k-mer profiling workflow (VGP 1 or 2) and a contiging workflow (VGP 3,4 or 5).

Type: Galaxy

Creator: Galaxy, VGP

Submitter: WorkflowHub Bot

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