Workflows

An example Workflow RO-Crate, showing a Galaxy workflow with an abstract CWL description and diagram. This Crate is deliberately excessively populated to show the exensible possibilities (e.g. including a BioCompute Object and a Planemo test), refer to the Workflow RO-Crate profile for minimal requirements.

V-pipe is a snakemake pipeline designed for analysing NGS data of short viral genomes.

This PyCOMPSs workflow tutorial aims to illustrate the process of setting up a simulation system containing a protein, step by step, using the BioExcel Building Blocks library (biobb) in PyCOMPSs for execution on HPC. Three variants of the MD Setup workflows are included, supporting a list of structures, a list of mutations, or a cumulative set of mutations.

Workflow for quality assessment of paired reads and classification using NGTax 2.0 and functional annotation using picrust2. In addition files are exported to their respective subfolders for easier data management in a later stage. Steps:

• FastQC (read quality control)
• NGTax 2.0
• Picrust 2
• Export module for ngtax

This PyCOMPSs workflow tutorial aims to illustrate the process of setting up a simulation system containing a protein, step by step, using the BioExcel Building Blocks library (biobb) in PyCOMPSs for execution on HPC. Three variants of the MD Setup workflows are included, supporting a list of structures, a list of mutations, or a cumulative set of mutations.

RO-Crate containing execution provenance about the MaxQuant-Workflow that analyze label-free data with MaxQuant based on Nextflow, running with SDRF implemented. Normalization and statistical comparisons using NormalyzerDE are conducted on the MaxQuant result

CWL version of the md_list.cwl workflow for HPC. This performs a system setup and runs a molecular dynamics simulation on the structure passed to this workflow. This workflow uses the md_gather.cwl sub-workflow to gather the outputs together to return these. To work with more than one structure this workflow can be called from either the md_launch.cwl workflow, or the md_launch_mutate.cwl workflow. These use scatter for parallelising the workflow. md_launch.cwl operates on a list of individual ...