Merge pull request #26 from BethYates/patch-1

Update genome-note-24.md

content/BGA24/sessions/genome-note-24.md

@@ -18,12 +18,42 @@ Wellcome Sanger Institute
 
 - [Bethan Yates](https://uk.linkedin.com/in/bethanyates)
 - [Tyler Chafin](https://www.sanger.ac.uk/person/chafin-tyler/)
-- [Matthieu Muffato](https://www.sanger.ac.uk/person/muffato-matthieu/)
 
 ## Description
 
 In this session you will learn how to automatically generate content for genome note publications using our suite of [ToL analysis pipelines](https://pipelines.tol.sanger.ac.uk).
 
+## Part 1: An introduction to Genome Notes
+
+By the end of this part you will have:
+
+1. Obtained an overview of the Tree of Life programme and our genome note concept
+2. Understood the purpose of a genome note and the information it reports
+3. Gained an idea of why automating genome note production is important and how this can be achieved
+
+## Part 2: Hands on - Running the sanger-tol/genomenote pipeline and exploring the outputs
+
+By the end of this part you will be able to:
+
+1. Run the sanger-tol/genomenote pipeline to produce a genome note document
+2. Understand how to use the pipeline to generate genome notes for your own genomes
+3. Gained an idea of how different pipelines can be combined to go from raw sequencing data to a publication reporting a genome assembly
+
+## The nextflow command to run the pipeline
+
+    nextflow run genomenote/main.nf \
+    -profile docker,arm \
+    -params-file assets/BGA-test.json \
+    --outdir BGA_test_results
+
+## Useful links 
+
+- The [sanger-tol/genomenote pipeline](https://pipelines.tol.sanger.ac.uk/). 
+- The published [genome note](https://wellcomeopenresearch.org/articles/9-539) for the species used in this session.
+- The HiGlass link to the [Hi-C map](https://genome-note-higlass.tol.sanger.ac.uk/l/?d=N0lSy7fGQ7SSE1afN54MCg) for the species used in this session.
+- The [Blobtool viewer](https://blobtoolkit.genomehubs.org/view/GCA_963859965.1/dataset/GCA_963859965.1/blob#Filters) for the species used in this session.
+- The [Genome After Party](https://gap.cog.sanger.ac.uk/Ceramica_pisi/) for the species used in this session.
+
 ## Prerequisites
 
 1. Familiarity with linux command line basics (cd, mv, rm)