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 96533912e25300bf0344dc44147c87db6d7ae3fe..c96a4951a5f1a9e9cbf1f67d3938f2e91d1b3bf6 100644 (file)
--- a/lesson3/answers/featureCounts.cwl
+++ b/lesson3/answers/featureCounts.cwl
@@ -20,7 +20,7 @@ arguments: [-T, $(runtime.cores),
 outputs:
   featurecounts:
     type: File
 outputs:
   featurecounts:
     type: File

-      outputBinding:
+    outputBinding:

       glob: featurecounts.tsv
 
 ### 6. Running in a container
       glob: featurecounts.tsv
 
 ### 6. Running in a container

diff --git a/lesson3/answers/main.cwl b/lesson3/answers/main.cwl
index 7eaf62ee9429b9e62c901b4051f00fd94a935149..937dd3a966107e43da0af43704c32e9cc6e97bcf 100644 (file)
--- a/lesson3/answers/main.cwl
+++ b/lesson3/answers/main.cwl
@@ -39,10 +39,10 @@ steps:
       ResourceRequirement:
         ramMin: 500
     run: featureCounts.cwl
       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:
 
 outputs:
   qc_html:


@@ -55,4 +55,4 @@ outputs:
   ### 8. Adding it to the workflow
   featurecounts:
     type: File
   ### 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 9bd5a7089e3ddf8da69865447067a9cfa3917540..f24bce49c82d3f8bf9dc9dc8e1e11943489b6b29 100644 (file)
--- a/lesson3/lesson3.md
+++ b/lesson3/lesson3.md
@@ -89,7 +89,7 @@ output directory called `featurecounts.tsv`
 outputs:
   featurecounts:
     type: File
 outputs:
   featurecounts:
     type: File

-      outputBinding:
+    outputBinding:

       glob: featurecounts.tsv
 ```
 
       glob: featurecounts.tsv
 ```
 


@@ -162,10 +162,10 @@ steps:
       ResourceRequirement:
         ramMin: 500
     run: featureCounts.cwl
       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:
 ```
 
 We will add the result from featurecounts to the output:


@@ -175,7 +175,7 @@ outputs:
   ...
   featurecounts:
     type: File
   ...
   featurecounts:
     type: File

-      outputSource: featureCounts/featurecounts
+    outputSource: featureCounts/featurecounts

 ```
 
 You should now be able to re-run the workflow and it will run the
 ```
 
 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 c46b568be63af4f105bc2319850bd9e87cda2696..3c2d79e887d48fb825c9d31ce20bf6048a1616b7 100644 (file)
--- a/lesson4/answers/part1/alignment.cwl
+++ b/lesson4/answers/part1/alignment.cwl
@@ -38,10 +38,10 @@ steps:
       ResourceRequirement:
         ramMin: 500
     run: featureCounts.cwl
       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:
 
 outputs:
   qc_html:


@@ -53,4 +53,4 @@ outputs:
 
   featurecounts:
     type: File
 
   featurecounts:
     type: File

-      outputSource: featureCounts/featurecounts
+    outputSource: featureCounts/featurecounts

diff --git a/lesson4/answers/part1/featureCounts.cwl b/lesson4/answers/part1/featureCounts.cwl
index 4407ec9119a7fc066982390aafe4444491223a36..eade371d402267e305104d0f6c494330ed387dcc 100644 (file)
--- a/lesson4/answers/part1/featureCounts.cwl
+++ b/lesson4/answers/part1/featureCounts.cwl
@@ -15,7 +15,7 @@ arguments: [-T, $(runtime.cores),
 outputs:
   featurecounts:
     type: File
 outputs:
   featurecounts:
     type: File

-      outputBinding:
+    outputBinding:

       glob: featurecounts.tsv
 
 hints:
       glob: featurecounts.tsv
 
 hints:

diff --git a/lesson4/answers/part2/alignment.cwl b/lesson4/answers/part2/alignment.cwl
index c46b568be63af4f105bc2319850bd9e87cda2696..3c2d79e887d48fb825c9d31ce20bf6048a1616b7 100644 (file)
--- a/lesson4/answers/part2/alignment.cwl
+++ b/lesson4/answers/part2/alignment.cwl
@@ -38,10 +38,10 @@ steps:
       ResourceRequirement:
         ramMin: 500
     run: featureCounts.cwl
       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:
 
 outputs:
   qc_html:


@@ -53,4 +53,4 @@ outputs:
 
   featurecounts:
     type: File
 
   featurecounts:
     type: File

-      outputSource: featureCounts/featurecounts
+    outputSource: featureCounts/featurecounts

diff --git a/lesson4/answers/part2/featureCounts.cwl b/lesson4/answers/part2/featureCounts.cwl
index 4407ec9119a7fc066982390aafe4444491223a36..eade371d402267e305104d0f6c494330ed387dcc 100644 (file)
--- a/lesson4/answers/part2/featureCounts.cwl
+++ b/lesson4/answers/part2/featureCounts.cwl
@@ -15,7 +15,7 @@ arguments: [-T, $(runtime.cores),
 outputs:
   featurecounts:
     type: File
 outputs:
   featurecounts:
     type: File

-      outputBinding:
+    outputBinding:

       glob: featurecounts.tsv
 
 hints:
       glob: featurecounts.tsv
 
 hints:

diff --git a/lesson4/answers/part4/featureCounts.cwl b/lesson4/answers/part4/featureCounts.cwl
index 38ace83f9e9b6cac8829d2dbd142dc4ffe6eeb0c..22047e65a99649e103ae08efcf1be7079f6ec185 100644 (file)
--- a/lesson4/answers/part4/featureCounts.cwl
+++ b/lesson4/answers/part4/featureCounts.cwl
@@ -18,7 +18,7 @@ arguments: [-T, $(runtime.cores),
 outputs:
   featurecounts:
     type: File
 outputs:
   featurecounts:
     type: File

-      outputBinding:
+    outputBinding:

       glob: featurecounts.tsv
 
 hints:
       glob: featurecounts.tsv
 
 hints:

diff --git a/lesson4/answers/part4/main.cwl b/lesson4/answers/part4/main.cwl
index fcbb235dfc4c8f9487282c07f00475f9bb111c1e..24d0bee41957bb09a08871997687acea79e03e82 100644 (file)
--- a/lesson4/answers/part4/main.cwl
+++ b/lesson4/answers/part4/main.cwl
@@ -16,7 +16,7 @@ steps:
       fq: fq
       genome: genome
       gtf: gtf
       fq: fq
       genome: genome
       gtf: gtf

-    out: [qc_html, bam_sorted_indexed, featurecounts]
+    out: [qc_html, bam_sorted_indexed]

 
   ### 4. Combining results
   featureCounts:
 
   ### 4. Combining results
   featureCounts:

diff --git a/lesson5/answers/featureCounts.cwl b/lesson5/answers/featureCounts.cwl
index 681697e9bac2aab5f1cb3874b8c71c136d1fd6b4..a17163f16a151e3da88672f62d809aac97682a14 100644 (file)
--- a/lesson5/answers/featureCounts.cwl
+++ b/lesson5/answers/featureCounts.cwl
@@ -17,7 +17,7 @@ arguments: [-T, $(runtime.cores),
 outputs:
   featurecounts:
     type: File
 outputs:
   featurecounts:
     type: File

-      outputBinding:
+    outputBinding:

       glob: featurecounts.tsv
 
 hints:
       glob: featurecounts.tsv
 
 hints:

diff --git a/lesson5/answers/main.cwl b/lesson5/answers/main.cwl
index e934079722bc5411b3aa43bfce095fce863ed36d..97461ce437f510061ced436eaf19e9bea7155669 100644 (file)
--- a/lesson5/answers/main.cwl
+++ b/lesson5/answers/main.cwl
@@ -15,7 +15,7 @@ steps:
       fq: fq
       genome: genome
       gtf: gtf
       fq: fq
       genome: genome
       gtf: gtf

-    out: [qc_html, bam_sorted_indexed, featurecounts]
+    out: [qc_html, bam_sorted_indexed]

 
   featureCounts:
     requirements:
 
   featureCounts:
     requirements: