formatting

[rnaseq-cwl-training.git] / lesson4 / lesson4.md

diff --git a/lesson4/lesson4.md b/lesson4/lesson4.md
index 447726d88bad9e48849a445f48fcf39e5178cd8c..6aa45de54b98f3ac44a585eb4bba587a6aa5a670 100644 (file)
--- a/lesson4/lesson4.md
+++ b/lesson4/lesson4.md
@@ -3,7 +3,7 @@
 Analyzing a single sample is great, but in the real world you probably
 have a batch of samples that you need to analyze and then compare.
 
-1. Subworkflows
+### 1. Subworkflows
 
 In addition to running command line tools, a workflow step can also
 execute another workflow.
@@ -48,7 +48,7 @@ requirements:
 If you run this workflow, you will get exactly the same results as
 before, we've just wrapped the inner workflow with an outer workflow.
 
-2. Scattering
+### 2. Scattering
 
 The wrapper lets us do something useful.  We can modify the outer
 workflow to accept a list of files, and then invoke the inner workflow
@@ -104,7 +104,7 @@ requirements:
   ScatterFeatureRequirement: {}
 ```
 
-3. Running with list inputs
+### 3. Running with list inputs
 
 The `fq` parameter needs to be a list.  You write a list in yaml by
 starting each list item with a dash.  Example `main-input.yaml`
@@ -139,7 +139,7 @@ gtf:
 
 Now you can run the workflow the same way as in Lesson 2.
 
-4. Combining results
+### 4. Combining results
 
 Each instance of the alignment workflow produces its own featureCounts
 file.  However, to be able to compare results easily, we need them a