From 1ead988de359a7ffb155615473fd03f5ab9c735d Mon Sep 17 00:00:00 2001
From: Peter Amstutz <peter.amstutz@curii.com>
Date: Fri, 15 Jan 2021 15:31:23 -0500
Subject: [PATCH] Starting the lesson.

---
 README => README.md                            | 18 ++++++++++++++++++
 lesson1/lesson1.md                             |  3 +++
 .../rnaseq_analysis_on_input_file.sh           |  0
 3 files changed, 21 insertions(+)
 rename README => README.md (64%)
 create mode 100644 lesson1/lesson1.md
 rename {scripts => lesson1}/rnaseq_analysis_on_input_file.sh (100%)

diff --git a/README b/README.md
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rename from README
rename to README.md
index 5a995d4..fd9a630 100644
--- a/README
+++ b/README.md
@@ -1,3 +1,21 @@
+
+# Downloading reference data
+
+```
+mkdir rnaseq
+cd rnaseq
+wget --mirror --no-parent --no-host --cut-dirs=1 https://download.pirca.arvadosapi.com/c=pirca-4zz18-sa9s62lzc00jeds/
+```
+
+# Building the Docker image
+
+```
+cd dockerfile
+docker build -t cwl-training-rnaseq-tools .
+```
+
+# Acknowledgements
+
 These CWL lessons are based on "Introduction to RNA-seq using
 high-performance computing (HPC)" lessons developed by members of the
 teaching team at the Harvard Chan Bioinformatics Core (HBC) and
diff --git a/lesson1/lesson1.md b/lesson1/lesson1.md
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+# Turning a bash script into a workflow
+
+In this lesson we will turn `rnaseq_analysis_on_input_file.sh` into a workflow.
diff --git a/scripts/rnaseq_analysis_on_input_file.sh b/lesson1/rnaseq_analysis_on_input_file.sh
similarity index 100%
rename from scripts/rnaseq_analysis_on_input_file.sh
rename to lesson1/rnaseq_analysis_on_input_file.sh
-- 
2.30.2