Workflows
What is a Workflow?Filters
Code for the high risk autism phenotype paper
Much of the code in this repo originated from ASD High Risk Endophenotype Code Supplement and was written by Sebastian Urchs and Hien Nguyen.
Data availability
All data to reproduce the analysis can be downloaded from
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Digitial Twin Component for Earthquakes (DTC-E) WorkFlow 1 (WF7501) uses new data to create a multi-scale model of the Earth, which is used to update the REVEAL/CSEMv3 velocity model. The WF7501 workflow models an inversion-based update process for CSEMv3 (Computational Seismic Earth Model). Below is a simple explanation of the STEPs:
- ST750101 - Data Catalog Update: Collects external data sources and updates the database for further processing.
- ST750102 - Inversion Setup: Configures ...
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
This workflow perform the scaffolding of a genome assemble using HiC data with YAHS. Part of the VGP set of workflows.
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 ...