From: Peter Amstutz <peter.amstutz@curii.com>
Date: Mon, 25 Jan 2021 20:58:41 +0000 (-0500)
Subject: Formatting
X-Git-Url: https://git.arvados.org/rnaseq-cwl-training.git/commitdiff_plain/a1187af77182f7f9b4719e361eae3ae4fade6d7c

Formatting

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

diff --git a/lesson1/lesson1.md b/lesson1/lesson1.md
index 8163823..f394c90 100644
--- a/lesson1/lesson1.md
+++ b/lesson1/lesson1.md
@@ -33,7 +33,7 @@ git submodule add https://github.com/common-workflow-library/bio-cwl-tools.git
 
 ## Writing the workflow
 
-### 1.
+### 1. File header
 
 Create a new file "main.cwl"
 
diff --git a/lesson2/lesson2.md b/lesson2/lesson2.md
index 0df5811..c1107c2 100644
--- a/lesson2/lesson2.md
+++ b/lesson2/lesson2.md
@@ -1,6 +1,6 @@
 # Running and debugging a workflow
 
-1. The input parameter file
+### 1. The input parameter file
 
 CWL input values are provided in the form of a YAML or JSON file.
 Create one by right clicking on the explorer, select "New File" and
@@ -14,46 +14,37 @@ When setting inputs, Files and Directories are given as an object with
 `class: File` or `class: Directory`.  This distinguishes them from
 plain strings that may or may not be file paths.
 
-
-## Arvados
+Note: if you don't have example sequence data or the STAR index files, see the Appendix below.
 
 ```
 fq:
   class: File
-  location: keep:9178fe1b80a08a422dbe02adfd439764+925/raw_fastq/Mov10_oe_1.subset.fq
+  location: rnaseq/raw_fastq/Mov10_oe_1.subset.fq
   format: http://edamontology.org/format_1930
 genome:
   class: Directory
-  location: keep:02a12ce9e2707610991bd29d38796b57+2912
+  location: hg19-chr1-STAR-index
 gtf:
   class: File
-  location: keep:9178fe1b80a08a422dbe02adfd439764+925/reference_data/chr1-hg19_genes.gtf
+  location: rnaseq/reference_data/chr1-hg19_genes.gtf
 ```
 
-## Generic
-
-Note: if you don't have example sequence data or the STAR index files, see the Appendix below.
+On Arvados, do this:
 
 ```
 fq:
   class: File
-  location: rnaseq/raw_fastq/Mov10_oe_1.subset.fq
+  location: keep:9178fe1b80a08a422dbe02adfd439764+925/raw_fastq/Mov10_oe_1.subset.fq
   format: http://edamontology.org/format_1930
 genome:
   class: Directory
-  location: hg19-chr1-STAR-index
+  location: keep:02a12ce9e2707610991bd29d38796b57+2912
 gtf:
   class: File
-  location: rnaseq/reference_data/chr1-hg19_genes.gtf
+  location: keep:9178fe1b80a08a422dbe02adfd439764+925/reference_data/chr1-hg19_genes.gtf
 ```
 
-2. Running the workflow
-
-## Arvados
-
-In vscode, select "main.cwl" and then choose "Terminal -> Run task -> Run CWL workflow on Arvados"
-
-## Generic
+### 2. Running the workflow
 
 Type this into the terminal:
 
@@ -61,7 +52,9 @@ Type this into the terminal:
 cwl-runner main.cwl main-input.yaml
 ```
 
-3. Debugging the workflow
+On Arvados with vscode, select "main.cwl" and then choose "Terminal -> Run task -> Run CWL workflow on Arvados"
+
+### 3. Debugging the workflow
 
 A workflow can fail for many reasons: some possible reasons include
 bad input, bugs in the code, or running out memory.  In this case, the
@@ -89,7 +82,7 @@ Container exited with code: 137
 
 If this happens, you will need to request more RAM.
 
-4. Setting runtime RAM requirements
+### 4. Setting runtime RAM requirements
 
 By default, a step is allocated 256 MB of RAM.  From the STAR error message:
 
@@ -116,7 +109,7 @@ Resource requirements you can set include:
 
 After setting the RAM requirements, re-run the workflow.
 
-5. Workflow results
+### 5. Workflow results
 
 The CWL runner will print a results JSON object to standard output.  It will look something like this (it may include additional fields).