Workflows
What is a Workflow?Filters
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: Nextflow
Creators: No author provided, Hadrien Gourlé, Daniel Straub, Sabrina Krakau
Submitter: WorkflowHub Bot
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 ...
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:
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low-resolution tissue segmentation to select areas for further processing;
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high-resolution tissue segmentation to refine borders - it uses step 1 as input;
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high-resolution normal/cancer classification - it uses step 1 as input.
Tissue segmentation workflow
This workflow performs tissue segmentation on H&E whole slide images using AI.
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.