Virus genome assembly with Unicycler and Spades,
The 2 assemblers works in parallel. The graph visualization is made with Bandage.
workflow git repository : https://github.com/fjrmoreews/cwl-workflow-SARS-CoV-2/blob/master/Assembly/workflow/assembly-wf-virus.cwl
Based on https://github.com/galaxyproject/SARS-CoV-2/blob/master/genomics/2-Assembly/as_wf.png
Type: Common Workflow Language
Submitter: francois moreews
Analysis of variation within individual COVID-19 samples
using bowtie2, bwa, fastp, multiqc , picard ,samtools, snpEff
Workflow, tools and data are available on https://github.com/fjrmoreews/cwl-workflow-SARS-CoV-2/tree/master/Variation
This worklow was ported into CWL from a Galaxy Workflow
( https://github.com/galaxyproject/SARS-CoV-2/tree/master/genomics/4-Variation migrated to CWL).
The tutorial for this workflow can be found on [Galaxy Training Network](https://training.galaxyproject.org/training-material/topics/climate/tutorials/climate-101/tutorial.html)
Creator: Anne Claire Fouilloux
Submitter: Bert Droesbeke