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[rnaseq-cwl-training.git] / _episodes / 02-workflow.md

diff --git a/_episodes/02-workflow.md b/_episodes/02-workflow.md
index 8e76a006d1feeac272b4f6cf41337f9e095b1e57..64851c50fda2491661d8597177d63b96261e1da2 100644 (file)
--- a/_episodes/02-workflow.md
+++ b/_episodes/02-workflow.md
@@ -317,13 +317,16 @@ correspond to the command line parmeters from our source script.
 > correspond to the command line arguments used in the source script:
 > `--runThreadN`, `--genomeDir`, `--outSAMtype`, and
 > `--outSAMunmapped`.  Also identify the name of the output parameter.
-> Use these to write the STAR step.
 >
 > > ## Solution
 > >
-> > input parameter name: RunThreadN, GenomeDir, ForwardReads, OutSAMtype, SortedByCoordinate, OutSAMunmapped
+> > * `--runThreadN` → `RunThreadN`
+> > * `--genomeDir` → `GenomeDir`
+> > * `--readFilesIn` → `ForwardReads`
+> > * `--outSAMtype` → `OutSAMtype`, `SortedByCoordinate`
+> > * `--outSAMunmapped` → `OutSAMunmapped`
 > >
-> > output parameter name: alignment
+> > output parameter name: `alignment`
 > {: .solution}
 {: .challenge}
 
@@ -359,7 +362,7 @@ correspond to the command line parmeters from our source script.
 
 > ## Exercise
 >
-> Using the input and output parameters identified in the last
+> Using the input and output parameters identified in the previous
 > exercise, write the `run`, `in` and `out` sections of the STAR step.
 >
 > > ## Solution
@@ -450,5 +453,5 @@ outputs:
 {: .language-yaml }
 
 > ## Episode solution
-> * <a href="{% link ../assets/answers/ep2/main.cwl %}">main.cwl</a>
+> * <a href="../assets/answers/ep2/main.cwl">main.cwl</a>
 {: .solution}