working on adapting Bioinformatics.ca annual Cancer Genomics workshop into Galaxy. Fixes gallantries/organisation#17

====== TODOs ======

Infra

• move tutorials to the relevant different topics
• create a synthetic topic for cancer (for all tutorials with the tag "cancer")
• create learning path for Bioinformatics.ca tutorials

Content

• Module1: Introduction slides
  • Slides
  • Slides speaker notes (for automatic video)
• Module 2: Data, formats and Databases
  • Slides
  • Slides speaker notes
  • Slides 2: Viewing Cancer Alignments in a Genome Browser
  • Slides 2 speaker notes
  • Tutorial
• Module 3: Genome Alignment
  • Slides
  • Slides speaker notes
  • Tutorial
  • maybe: add missing GATK tools to Galaxy
• Module 4: Somatic Genomic Alteration
  • Slides
  • Slides speaker notes
  • Tutorial
• Module 5: Single Cell Genomics - DNA
  • Slides
  • Slides speaker notes
  • Tutorial
• Module 6: Gene Expression Profiling
  • Slides
  • Slides speaker notes
  • Tutorial
• Module 7: Single Cell Genomics - RNA
  • Slides
  • Slides speaker notes
  • Tutorial
• Module 8: Genes to Pathways
  • Slides
  • Slides speaker notes
  • Tutorial
• Module 9: Genes to Networks
  • Slides
  • Slides speaker notes
  • Tutorial
• Module 10: Integration of Clinical Data
  • Slides
  • Slides speaker notes
  • Tutorial
• Module 11: Multi-omic data integration
  • Slides
  • Slides speaker notes
  • Tutorial

====== Misc Notes ======

Module 3: Genome Alignment

• Replaced trimmomatic with Trim Galore! for technical reasons
• FASTQC does not detect any adapters? trim galore only if you set it to overlap of 1?
• GATK4 tools not in Galaxy due to historically problematic license, alternative tools for last steps in tutorial? Licences is now better so we could put them in Galaxy after all? SRMA could be alternative to GATK indelrealigner, but is a built-in Galaxy tool and not working