From: Peter Amstutz <peter.amstutz@curii.com>
Date: Mon, 25 Jan 2021 21:01:42 +0000 (-0500)
Subject: formatting
X-Git-Url: https://git.arvados.org/rnaseq-cwl-training.git/commitdiff_plain/229b9409628272290071af003f2fb05df06e1460

formatting

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
---

diff --git a/lesson3/lesson3.md b/lesson3/lesson3.md
index b7e3334..622f446 100644
--- a/lesson3/lesson3.md
+++ b/lesson3/lesson3.md
@@ -4,18 +4,18 @@ It is time to add the last step in the analysis.
 
 This will use the "featureCounts" tool from the "subread" package.
 
-# Writing the tool wrapper
+### 1. File header
 
-1. Create a new file "featureCounts.cwl"
+Create a new file "featureCounts.cwl"
 
-2. Start with this header
+Start with this header
 
 ```
 cwlVersion: v1.2
 class: CommandLineTool
 ```
 
-3. Command line tool inputs
+### 2. Command line tool inputs
 
 A CommandLineTool describes a single invocation of a command line program.
 
@@ -40,7 +40,7 @@ inputs:
   counts_input_bam: File
 ```
 
-4. Specifying the program to run
+### 3. Specifying the program to run
 
 Give the name of the program to run in `baseCommand`.
 
@@ -48,7 +48,7 @@ Give the name of the program to run in `baseCommand`.
 baseCommand: featureCounts
 ```
 
-5. Command arguments
+### 4. Command arguments
 
 The easiest way to describe the command line is with an `arguments`
 section.  This takes a comma-separated list of command line arguments.
@@ -68,7 +68,7 @@ arguments: [-T, $(runtime.cores),
 			$(inputs.counts_input_bam)]
 ```
 
-6. Outputs section
+### 5. Outputs section
 
 In CWL, you must explicitly identify the outputs of a program.  This
 associates output parameters with specific files, and enables the
@@ -93,7 +93,7 @@ outputs:
 	  glob: featurecounts.tsv
 ```
 
-7. Running in a container
+### 6. Running in a container
 
 In order to run the tool, it needs to be installed.
 Using software containers, a tool can be pre-installed into a
@@ -123,7 +123,7 @@ hints:
     dockerPull: quay.io/biocontainers/subread:1.5.0p3--0
 ```
 
-8. Running a tool on its own
+### 7. Running a tool on its own
 
 When creating a tool wrapper, it is helpful to run it on its own to test it.
 
@@ -147,7 +147,7 @@ The invocation is also the same:
 cwl-runner featureCounts.cwl featureCounts.yaml
 ```
 
-9. Adding it to the workflow
+### 8. Adding it to the workflow
 
 Now that we have confirmed that it works, we can add it to our workflow.
 We add it to `steps`, connecting the output of samtools to
diff --git a/lesson4/lesson4.md b/lesson4/lesson4.md
index 447726d..6aa45de 100644
--- 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
diff --git a/lesson5/lesson5.md b/lesson5/lesson5.md
index 54df134..6a53398 100644
--- a/lesson5/lesson5.md
+++ b/lesson5/lesson5.md
@@ -1,6 +1,6 @@
 # Expressions
 
-1. Expressions on step inputs
+### 1. Expressions on step inputs
 
 You might have noticed that the output bam files are all named
 `Aligned.sortedByCoord.out.bam`.  This happens because because when we
@@ -53,7 +53,7 @@ adds the remainder of the string, which just is a dot `.`.  This is to
 separate the leading part of our filename from the "Aligned.bam"
 extension that will be added by STAR.
 
-2. Organizing output files into Directories
+### 2. Organizing output files into Directories
 
 You probably noticed that all the output files appear in the same
 directory.  You might prefer that each file appears in its own
@@ -139,7 +139,3 @@ outputs:
     type: File
     outputSource: featureCounts/featurecounts
 ```
-
-3. Other uses for expressions
-
-- Creating configuration files on the fly.