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[rnaseq-cwl-training.git] / _episodes / 05-scatter.md

diff --git a/_episodes/05-scatter.md b/_episodes/05-scatter.md
index 29039526c6432828ae0e7421ee3cf26784f9cce8..224fdc9ade45f644f39f7a9d13dd129e5b92827a 100644 (file)
--- a/_episodes/05-scatter.md
+++ b/_episodes/05-scatter.md
@@ -1,7 +1,7 @@
 ---
 title: "Analyzing Multiple Samples"
-teaching: 20
-exercises: 0
+teaching: 30
+exercises: 30
 questions:
 - "How can you run the same workflow over multiple samples?"
 objectives:
@@ -66,9 +66,19 @@ requirements:
 ```
 {: .language-yaml }
 
-If you run this workflow, you will get exactly the same results as
-before, as all we have done so far is to wrap the inner workflow with
-an outer workflow.
+> ## Running the workflow
+>
+> Run this workflow.  You should get exactly the same results as
+> before, as all we have done so far is to wrap the inner workflow with
+> an outer workflow.
+>
+{: .challenge }
+
+> ## Part 1 solution
+> * <a href="../assets/answers/ep5/part1/main.cwl">main.cwl</a>
+> * <a href="../assets/answers/ep5/part1/alignment.cwl">alignment.cwl</a>
+> * <a href="../assets/answers/ep5/part1/featureCounts.cwl">featureCounts.cwl</a>
+{: .solution}
 
 # Scattering
 
@@ -131,6 +141,12 @@ requirements:
 ```
 {: .language-yaml }
 
+> ## Part 2 solution
+> * <a href="../assets/answers/ep5/part2/main.cwl">main.cwl</a>
+> * <a href="../assets/answers/ep5/part2/alignment.cwl">alignment.cwl</a>
+> * <a href="../assets/answers/ep5/part2/featureCounts.cwl">featureCounts.cwl</a>
+{: .solution}
+
 # Input parameter lists
 
 The `fq` parameter needs to be a list.  You write a list in yaml by
@@ -165,8 +181,12 @@ gtf:
 ```
 {: .language-yaml }
 
-If you run the workflow, you will get results for each one of the
-input fastq files.
+> ## Running the workflow
+>
+> Run this workflow.  You will now get results for each one of the
+> input fastq files.
+>
+{: .challenge }
 
 # Combining results
 
@@ -231,5 +251,16 @@ outputs:
 ```
 {: .language-yaml }
 
-Run this workflow to get a single `featurecounts.tsv` file with a
-column for each bam file.
+> ## Running the workflow
+>
+> Run this workflow.  You will still have separate results from fastq
+> and and STAR, but now you will only have a single
+> `featurecounts.tsv` file with a column for each bam file.
+>
+{: .challenge }
+
+> ## Episode solution
+> * <a href="../assets/answers/ep5/part4/main.cwl">main.cwl</a>
+> * <a href="../assets/answers/ep5/part4/alignment.cwl">alignment.cwl</a>
+> * <a href="../assets/answers/ep5/part4/featureCounts.cwl">featureCounts.cwl</a>
+{: .solution}