X-Git-Url: https://git.arvados.org/rnaseq-cwl-training.git/blobdiff_plain/1dcbce0b09a71abaec4b1e72dd70a2f573e4dc6b..1b451366891e7fddcb408e5ae7a6a741292cdeee:/lesson1/lesson1.md

diff --git a/lesson1/lesson1.md b/lesson1/lesson1.md
index 060597a..4846d72 100644
--- a/lesson1/lesson1.md
+++ b/lesson1/lesson1.md
@@ -54,7 +54,18 @@ series of steps, and produce output values.
 
 For this analysis, the input parameters are the fastq file and the reference data required by STAR.
 
-In CWL, these are declared in the `inputs` section.
+In the original bash script, the following variables are declared:
+
+```
+# initialize a variable with an intuitive name to store the name of the input fastq file
+fq=$1
+
+# directory with genome reference FASTA and index files + name of the gene annotation file
+genome=rnaseq/reference_data
+gtf=rnaseq/reference_data/chr1-hg19_genes.gtf
+```
+
+In CWL, we will declare these variables in the `inputs` section.
 
 The inputs section lists each input parameter and its type.  Valid
 types include `File`, `Directory`, `string`, `boolean`, `int`, and