From: Peter Amstutz <peter.amstutz@curii.com>
Date: Tue, 26 Jan 2021 20:05:09 +0000 (-0500)
Subject: Fix typos
X-Git-Url: https://git.arvados.org/rnaseq-cwl-training.git/commitdiff_plain/aef896336dc93b17de519e6be6d2f8aaa586f82f

Fix typos

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

diff --git a/lesson3/answers/featureCounts.cwl b/lesson3/answers/featureCounts.cwl
index 9653391..c96a495 100644
--- a/lesson3/answers/featureCounts.cwl
+++ b/lesson3/answers/featureCounts.cwl
@@ -20,7 +20,7 @@ arguments: [-T, $(runtime.cores),
 outputs:
   featurecounts:
     type: File
-      outputBinding:
+    outputBinding:
       glob: featurecounts.tsv
 
 ### 6. Running in a container
diff --git a/lesson3/answers/main.cwl b/lesson3/answers/main.cwl
index 7eaf62e..937dd3a 100644
--- a/lesson3/answers/main.cwl
+++ b/lesson3/answers/main.cwl
@@ -39,10 +39,10 @@ steps:
       ResourceRequirement:
         ramMin: 500
     run: featureCounts.cwl
-      in:
-        counts_input_bam: samtools/bam_sorted_indexed
-        gtf: gtf
-      out: [featurecounts]
+    in:
+      counts_input_bam: samtools/bam_sorted_indexed
+      gtf: gtf
+    out: [featurecounts]
 
 outputs:
   qc_html:
@@ -55,4 +55,4 @@ outputs:
   ### 8. Adding it to the workflow
   featurecounts:
     type: File
-      outputSource: featureCounts/featurecounts
+    outputSource: featureCounts/featurecounts
diff --git a/lesson3/lesson3.md b/lesson3/lesson3.md
index 9bd5a70..f24bce4 100644
--- a/lesson3/lesson3.md
+++ b/lesson3/lesson3.md
@@ -89,7 +89,7 @@ output directory called `featurecounts.tsv`
 outputs:
   featurecounts:
     type: File
-      outputBinding:
+    outputBinding:
       glob: featurecounts.tsv
 ```
 
@@ -162,10 +162,10 @@ steps:
       ResourceRequirement:
         ramMin: 500
     run: featureCounts.cwl
-      in:
-        counts_input_bam: samtools/bam_sorted_indexed
-        gtf: gtf
-      out: [featurecounts]
+    in:
+      counts_input_bam: samtools/bam_sorted_indexed
+      gtf: gtf
+    out: [featurecounts]
 ```
 
 We will add the result from featurecounts to the output:
@@ -175,7 +175,7 @@ outputs:
   ...
   featurecounts:
     type: File
-      outputSource: featureCounts/featurecounts
+    outputSource: featureCounts/featurecounts
 ```
 
 You should now be able to re-run the workflow and it will run the
diff --git a/lesson4/answers/part1/alignment.cwl b/lesson4/answers/part1/alignment.cwl
index c46b568..3c2d79e 100644
--- a/lesson4/answers/part1/alignment.cwl
+++ b/lesson4/answers/part1/alignment.cwl
@@ -38,10 +38,10 @@ steps:
       ResourceRequirement:
         ramMin: 500
     run: featureCounts.cwl
-      in:
-        counts_input_bam: samtools/bam_sorted_indexed
-        gtf: gtf
-      out: [featurecounts]
+    in:
+      counts_input_bam: samtools/bam_sorted_indexed
+      gtf: gtf
+    out: [featurecounts]
 
 outputs:
   qc_html:
@@ -53,4 +53,4 @@ outputs:
 
   featurecounts:
     type: File
-      outputSource: featureCounts/featurecounts
+    outputSource: featureCounts/featurecounts
diff --git a/lesson4/answers/part1/featureCounts.cwl b/lesson4/answers/part1/featureCounts.cwl
index 4407ec9..eade371 100644
--- a/lesson4/answers/part1/featureCounts.cwl
+++ b/lesson4/answers/part1/featureCounts.cwl
@@ -15,7 +15,7 @@ arguments: [-T, $(runtime.cores),
 outputs:
   featurecounts:
     type: File
-      outputBinding:
+    outputBinding:
       glob: featurecounts.tsv
 
 hints:
diff --git a/lesson4/answers/part2/alignment.cwl b/lesson4/answers/part2/alignment.cwl
index c46b568..3c2d79e 100644
--- a/lesson4/answers/part2/alignment.cwl
+++ b/lesson4/answers/part2/alignment.cwl
@@ -38,10 +38,10 @@ steps:
       ResourceRequirement:
         ramMin: 500
     run: featureCounts.cwl
-      in:
-        counts_input_bam: samtools/bam_sorted_indexed
-        gtf: gtf
-      out: [featurecounts]
+    in:
+      counts_input_bam: samtools/bam_sorted_indexed
+      gtf: gtf
+    out: [featurecounts]
 
 outputs:
   qc_html:
@@ -53,4 +53,4 @@ outputs:
 
   featurecounts:
     type: File
-      outputSource: featureCounts/featurecounts
+    outputSource: featureCounts/featurecounts
diff --git a/lesson4/answers/part2/featureCounts.cwl b/lesson4/answers/part2/featureCounts.cwl
index 4407ec9..eade371 100644
--- a/lesson4/answers/part2/featureCounts.cwl
+++ b/lesson4/answers/part2/featureCounts.cwl
@@ -15,7 +15,7 @@ arguments: [-T, $(runtime.cores),
 outputs:
   featurecounts:
     type: File
-      outputBinding:
+    outputBinding:
       glob: featurecounts.tsv
 
 hints:
diff --git a/lesson4/answers/part4/featureCounts.cwl b/lesson4/answers/part4/featureCounts.cwl
index 38ace83..22047e6 100644
--- a/lesson4/answers/part4/featureCounts.cwl
+++ b/lesson4/answers/part4/featureCounts.cwl
@@ -18,7 +18,7 @@ arguments: [-T, $(runtime.cores),
 outputs:
   featurecounts:
     type: File
-      outputBinding:
+    outputBinding:
       glob: featurecounts.tsv
 
 hints:
diff --git a/lesson4/answers/part4/main.cwl b/lesson4/answers/part4/main.cwl
index fcbb235..24d0bee 100644
--- a/lesson4/answers/part4/main.cwl
+++ b/lesson4/answers/part4/main.cwl
@@ -16,7 +16,7 @@ steps:
       fq: fq
       genome: genome
       gtf: gtf
-    out: [qc_html, bam_sorted_indexed, featurecounts]
+    out: [qc_html, bam_sorted_indexed]
 
   ### 4. Combining results
   featureCounts:
diff --git a/lesson5/answers/featureCounts.cwl b/lesson5/answers/featureCounts.cwl
index 681697e..a17163f 100644
--- a/lesson5/answers/featureCounts.cwl
+++ b/lesson5/answers/featureCounts.cwl
@@ -17,7 +17,7 @@ arguments: [-T, $(runtime.cores),
 outputs:
   featurecounts:
     type: File
-      outputBinding:
+    outputBinding:
       glob: featurecounts.tsv
 
 hints:
diff --git a/lesson5/answers/main.cwl b/lesson5/answers/main.cwl
index e934079..97461ce 100644
--- a/lesson5/answers/main.cwl
+++ b/lesson5/answers/main.cwl
@@ -15,7 +15,7 @@ steps:
       fq: fq
       genome: genome
       gtf: gtf
-    out: [qc_html, bam_sorted_indexed, featurecounts]
+    out: [qc_html, bam_sorted_indexed]
 
   featureCounts:
     requirements: