---
title: "Analyzing Multiple Samples"
-teaching: 20
-exercises: 0
+teaching: 30
+exercises: 30
questions:
- "How can you run the same workflow over multiple samples?"
objectives:
```
{: .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="{{ relative_root_path }}{% link /assets/answers/ep5/part1/main.cwl %}">main.cwl</a>
+> * <a href="{{ relative_root_path }}{% link /assets/answers/ep5/part1/alignment.cwl %}">alignment.cwl</a>
+> * <a href="{{ relative_root_path }}{% link /assets/answers/ep5/part1/featureCounts.cwl %}">featureCounts.cwl</a>
+{: .solution}
# Scattering
```
{: .language-yaml }
+> ## Part 2 solution
+> * <a href="{{ relative_root_path }}{% link /assets/answers/ep5/part2/main.cwl %}">main.cwl</a>
+> * <a href="{{ relative_root_path }}{% link /assets/answers/ep5/part2/alignment.cwl %}">alignment.cwl</a>
+> * <a href="{{ relative_root_path }}{% link /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
```
{: .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
```
{: .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}