COVID-19: variation analysis on ARTIC PE data

The workflow for Illumina-sequenced ARTIC data builds on the RNASeq workflow for paired-end data using the same steps for mapping and variant calling, but adds extra logic for trimming ARTIC primer sequences off reads with the ivar package. In addition, this workflow uses ivar also to identify amplicons affected by ARTIC primer-binding site mutations and, if possible, excludes reads derived from such ...

COVID-19: variation analysis on ARTIC ONT data

This workflow for ONT-sequenced ARTIC data is modeled after the alignment/variant-calling steps of the ARTIC pipeline. It performs, essentially, the same steps as that pipeline’s minion command, i.e. read mapping with minimap2 and variant calling with medaka. Like the Illumina ARTIC workflow it uses ivar for primer trimming. Since ONT-sequenced reads have a much ...

COVID-19: consensus construction

This workflow aims at generating reliable consensus sequences from variant calls according to transparent criteria that capture at least some of the complexity of variant calling.

It takes a collection of VCFs and a collection of the corresponding aligned reads (for the purpose of calculating genome-wide coverage) such as produced by any of the four variant calling workflows in https://github.com/galaxyproject/iwc/tree/main/workflows/sars-cov-2-variant-calling ...

Parallel Accession Download

Downloads fastq files for sequencing run accessions provided in a text file using fasterq-dump. Creates one job per listed run accession, and is therefore much faster and more robust to errors when many accessions need to be downloaded.

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 ...

Exome SAMtools Workflow

Summary

This tutorial aims to illustrate the process of protein-ligand docking, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the Mitogen-activated protein kinase 14 (p38-α) protein (PDB code 3HEC), a well-known Protein Kinase enzyme, in complex with the FDA-approved Imatinib, (PDB Ligand code STI, DrugBank Ligand Code DB00619), a small molecule kinase inhibitor used to treat certain types of cancer.

Workflow engine is a jupyter notebook. It ...