Add MRSA Nanopore assembly tutorial to AMR learning pathway

learning-pathways/amr-gene-detection.md

@@ -32,10 +32,8 @@ pathway:
     tutorials:
       - name: mrsa-illumina
         topic: assembly
-#      - name: mrsa-nanopore
-#        topic: assembly
-#      - name: hybrid-assembly
-#        topic: assembly
+      - name: mrsa-nanopore
+        topic: assembly
 
   - section: "Module: Genome annotation"
     description: |

topics/assembly/tutorials/mrsa-nanopore/tutorial.md

@@ -1,7 +1,7 @@
 ---
 layout: tutorial_hands_on
 
-title: Genome Assembly of MRSA using Oxford Nanopore MinION (and Illumina data if available)
+title: Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data)
 zenodo_link: 'https://zenodo.org/record/10669812'
 questions:
 - How to check the quality of the MinION data (together with Illumina data)?
@@ -311,7 +311,7 @@ For each run, **NanoPlot** generates 5 outputs:
    > > <solution-title></solution-title>
    > > 1. 3,400 bp to 5,451 bp, a 60.3% increase
    > > 2. A -2.0% decrease is not a very significant decrease. Our data was quite good to start with and didn't have many short reads which were removed (23.4%)
-   > > 3. The coverage is a measure of how many reads 'cover' on average a single base in the genome. If you divide the total reads by the genome size, you will get a number how many times your genomes could theoretically be ‘covered’ by reads.
+   > > 3. The coverage is a measure of how many reads 'cover' on average a single base in the genome. If you divide the total reads by the genome size, you will get a number how many times your genomes could theoretically be "covered" by reads.
    > > 4. Before $$ \frac{621,945,741}{2,900,000} = 214.4$$ and after $$ \frac{609,657,642}{2,900,000} = 210.2$$. This is *not* a very big decrease in coverage, so no cause for concern. Generally in sequencing experiments you have some minimum coverage you expect to see based on how much of your sample you sequenced. If it falls below that threshold it might be cause for concern.
    > >
    > {: .solution}

topics/assembly/tutorials/mrsa-nanopore/workflows/main-workflow-tests.yml

@@ -0,0 +1,25 @@
+- doc: Test outline for Genome-Assembly-of-MRSA-using-Oxford-Nanopore-MinION-(and-Illumina-data-if-available)
+  job:
+    Illumina reverse raw reads:
+      class: File
+      path: test-data/Illumina reverse raw reads.fastqsanger.bz2
+      filetype: fastqsanger.bz2
+    Illumina forward raw reads:
+      class: File
+      path: test-data/Illumina forward raw reads.fastqsanger.bz2
+      filetype: fastqsanger.bz2
+    Nanopore raw reads:
+      class: File
+      path: test-data/Nanopore raw reads.fastqsanger.bz2
+      filetype: fastqsanger.bz2
+  outputs:
+    quast_report_after_polishing:
+      path: test-data/quast_report_after_polishing.html
+    quast_report_before_polishing:
+      path: test-data/quast_report_before_polishing.html
+    nanoplot_after_filtering:
+      path: test-data/nanoplot_after_filtering.tabular
+    flye_assembly_info:
+      path: test-data/flye_assembly_info.tabular
+    nanoplot_before_filtering:
+      path: test-data/nanoplot_before_filtering.tabular