More text for lesson 5. Working on formatting.

[rnaseq-cwl-training.git] / lesson1 / lesson1.md

diff --git a/lesson1/lesson1.md b/lesson1/lesson1.md
index b989855ab8f7811e8c35e2dd823cbd9782ef21e7..8163823a57b61bcb5402a0bacb324c7edad4d06d 100644 (file)
--- a/lesson1/lesson1.md
+++ b/lesson1/lesson1.md
@@ -2,7 +2,7 @@
 
 In this lesson we will turn `rnaseq_analysis_on_input_file.sh` into a workflow.
 
-# Setting up
+## Setting up
 
 We will create a new git repository and import a library of existing
 tool definitions that will help us build our workflow.
@@ -11,19 +11,16 @@ tool definitions that will help us build our workflow.
 
 2. Create a new git repository to hold our workflow with this command:
 
-## Arvados
-
 ```
-git clone https://github.com/arvados/arvados-vscode-cwl-template.git rnaseq-cwl-training-exercises
+git init rnaseq-cwl-training-exercises
 ```
 
-## Generic
+On Arvados use this:
 
 ```
-git init rnaseq-cwl-training-exercises
+git clone https://github.com/arvados/arvados-vscode-cwl-template.git rnaseq-cwl-training-exercises
 ```
 
-
 3. Go to File->Open Folder and select rnaseq-cwl-training-exercises
 
 4. Go to the terminal window
@@ -34,11 +31,13 @@ git init rnaseq-cwl-training-exercises
 git submodule add https://github.com/common-workflow-library/bio-cwl-tools.git
 ```
 
-# Writing the workflow
+## Writing the workflow
+
+### 1.
 
-1. Create a new file "main.cwl"
+Create a new file "main.cwl"
 
-2. Start with this header.
+Start with this header.
 
 
 ```
@@ -47,7 +46,7 @@ class: Workflow
 label: RNAseq CWL practice workflow
 ```
 
-3. Workflow Inputs
+### 2. Workflow Inputs
 
 The purpose of a workflow is to consume some input parameters, run a
 series of steps, and produce output values.
@@ -80,7 +79,7 @@ inputs:
   gtf: File
 ```
 
-4. Workflow Steps
+### 3. Workflow Steps
 
 A workflow consists of one or more steps.  This is the `steps` section.
 
@@ -115,7 +114,7 @@ steps:
     out: [html_file]
 ```
 
-5. Running alignment with STAR
+### 4. Running alignment with STAR
 
 STAR has more parameters.  Sometimes we want to provide input values
 to a step without making them as workflow-level inputs.  We can do
@@ -137,7 +136,7 @@ this with `{default: N}`
     out: [alignment]
 ```
 
-6. Running samtools
+### 5. Running samtools
 
 The third step is to generate an index for the aligned BAM.
 
@@ -156,7 +155,7 @@ step will not run until the `STAR` step has completed successfully.
     out: [bam_sorted_indexed]
 ```
 
-7. featureCounts
+### 6. featureCounts
 
 As of this writing, the `subread` package that provides
 `featureCounts` is not available in bio-cwl-tools (and if it has been
@@ -164,7 +163,7 @@ added since writing this, let's pretend that it isn't there.)  We will
 dive into how to write a CWL wrapper for a command line tool in
 lesson 2.  For now, we will leave off the final step.
 
-8. Workflow Outputs
+### 7. Workflow Outputs
 
 The last thing to do is declare the workflow outputs in the `outputs` section.