Merge branch 'gh-pages' into no-side-effect-14

Author: mr-c

_episodes/11-records.md

@@ -32,9 +32,10 @@ parameters together to describe these two conditions.
 
 ~~~
 $ cwl-runner record.cwl record-job1.yml
-Workflow error:
-  Error validating input record, could not validate field `dependent_parameters` because
-  missing required field `itemB`
+Workflow error, try again with --debug for more information:
+Invalid job input record:
+record-job1.yml:1:1: the `dependent_parameters` field is not valid because
+                       missing required field `itemB`
 ~~~
 {: .output}
 
@@ -49,10 +50,28 @@ In the first example, you can't provide `itemA` without also providing `itemB`.
 
 ~~~
 $ cwl-runner record.cwl record-job2.yml
-[job 140566927111376] /home/example$ echo -A one -B two -C three
--A one -B two -C three
+record-job2.yml:6:3: invalid field `itemD`, expected one of: 'itemC'
+[job record.cwl] /home/example$ echo \
+    -A \
+    one \
+    -B \
+    two \
+    -C \
+    three > /home/example/output.txt
+[job record.cwl] completed success
+{
+    "example_out": {
+        "location": "file:///home/example/11-records/output.txt",
+        "basename": "output.txt",
+        "class": "File",
+        "checksum": "sha1$329fe3b598fed0dfd40f511522eaf386edb2d077",
+        "size": 23,
+        "path": "/home/example/output.txt"
+    }
+}
 Final process status is success
-{}
+$ cat output.txt
+-A one -B two -C three
 ~~~
 {: .output}
 
@@ -68,10 +87,27 @@ is added to the command line and `itemD` is ignored.
 
 ~~~
 $ cwl-runner record.cwl record-job3.yml
-[job 140606932172880] /home/example$ echo -A one -B two -D four
--A one -B two -D four
+[job record.cwl] /home/example$ echo \
+    -A \
+    one \
+    -B \
+    two \
+    -D \
+    four > /home/example/output.txt
+[job record.cwl] completed success
+{
+    "example_out": {
+        "location": "file:///home/example/output.txt",
+        "basename": "output.txt",
+        "class": "File",
+        "checksum": "sha1$77f572b28e441240a5e30eb14f1d300bcc13a3b4",
+        "size": 22,
+        "path": "/home/example/output.txt"
+    }
+}
 Final process status is success
-{}
+$ cat output.txt
+-A one -B two -D four
 ~~~
 {: .output}
 

_episodes/12-env.md

@@ -35,11 +35,23 @@ command line:
 
 ~~~
 $ cwl-runner env.cwl echo-job.yml
-[job 140710387785808] /home/example$ env
-PATH=/bin:/usr/bin:/usr/local/bin
+[job env.cwl] /home/example$ env > /home/example/output.txt
+[job env.cwl] completed success
+{
+    "example_out": {
+        "location": "file:///home/example/output.txt",
+        "basename": "output.txt",
+        "class": "File",
+        "checksum": "sha1$1ca16a840b14807b2fd3323022c476b06a150e2f",
+        "size": 94,
+        "path": "/home/example/output.txt"
+    }
+}
+Final process status is success
+$ cat output.txt
 HELLO=Hello world!
+PATH=/bin:/usr/bin:/usr/local/bin
+HOME=/home/example
 TMPDIR=/tmp/tmp63Obpk
-Final process status is success
-{}
 ~~~
 {: .output}

_episodes/13-expressions.md

@@ -49,10 +49,36 @@ We can then run `expression.cwl`:
 
 ~~~
 $ cwl-runner expression.cwl empty.yml
-[job 140000594593168] /home/example$ echo -A 2 -B baz -C 10 9 8 7 6 5 4 3 2 1
--A 2 -B baz -C 10 9 8 7 6 5 4 3 2 1
+[job expression.cwl] /home/example$ echo \
+    -A \
+    2 \
+    -B \
+    baz \
+    -C \
+    10 \
+    9 \
+    8 \
+    7 \
+    6 \
+    5 \
+    4 \
+    3 \
+    2 \
+    1 > /home/example/output.txt
+[job expression.cwl] completed success
+{
+    "example_out": {
+        "location": "file:///home/example/output.txt",
+        "basename": "output.txt",
+        "class": "File",
+        "checksum": "sha1$a739a6ff72d660d32111265e508ed2fc91f01a7c",
+        "size": 36,
+        "path": "/home/example/output.txt"
+    }
+}
 Final process status is success
-{}
+$ cat output.txt
+-A 2 -B baz -C 10 9 8 7 6 5 4 3 2 1
 ~~~
 {: .output}
 

_includes/cwl/11-records/record.cwl

@@ -32,5 +32,8 @@ inputs:
             type: string
             inputBinding:
               prefix: -D
-outputs: []
+outputs:
+  example_out:
+    type: stdout
+stdout: output.txt
 baseCommand: echo

_includes/cwl/12-env/env.cwl

@@ -9,4 +9,7 @@ requirements:
       HELLO: $(inputs.message)
 inputs:
   message: string
-outputs: []
+outputs:
+  example_out:
+    type: stdout
+stdout: output.txt

_includes/cwl/13-expressions/expression.cwl

@@ -8,7 +8,10 @@ requirements:
   - class: InlineJavascriptRequirement
 
 inputs: []
-outputs: []
+outputs:
+  example_out:
+    type: stdout
+stdout: output.txt
 arguments:
   - prefix: -A
     valueFrom: $(1+1)

_includes/cwl/conformance-test.yml

@@ -102,14 +102,54 @@
         size: 0
 
 # Section 11 depends on side-effects
-# Rest two examples in Section 11 depend on side-effects
 - doc: Test for section 11 (1st example)
   job: 11-records/record-job1.yml
   tool: 11-records/record.cwl
   should_fail: true
 
-# Section 12 depends on side-effects
-# Section 13 depends on side-effects
+- doc: Test for section 11 (2nd example)
+  job: 11-records/record-job2.yml
+  tool: 11-records/record.cwl
+  output:
+    example_out:
+      class: File
+      checksum: sha1$329fe3b598fed0dfd40f511522eaf386edb2d077
+      basename: output.txt
+      location: Any
+      size: 23
+
+- doc: Test for section 11 (3rd example)
+  job: 11-records/record-job3.yml
+  tool: 11-records/record.cwl
+  output:
+    example_out:
+      class: File
+      checksum: sha1$77f572b28e441240a5e30eb14f1d300bcc13a3b4
+      basename: output.txt
+      location: Any
+      size: 22
+
+# Section 12
+- doc: Test for section 12
+  job: 12-env/echo-job.yml
+  tool: 12-env/env.cwl
+  output:
+    example_out:
+      class: File
+      basename: output.txt
+      location: Any
+
+# Section 13
+- doc: Test for section 13
+  job: 13-expressions/empty.yml
+  tool: 13-expressions/expression.cwl
+  output:
+    example_out:
+      class: File
+      checksum: sha1$a739a6ff72d660d32111265e508ed2fc91f01a7c
+      basename: output.txt
+      location: Any
+      size: 36
 
 # Section 14
 - doc: Test for section 14
@@ -167,16 +207,16 @@
       location: Any
 
 # Section 19
-# See: Issue #48
-# - doc: Test for section 19
-#   job: 19-custom-types/custom-types.yml
-#   tool: 19-custom-types/costom-types.cwl
-#   output:
-#     i5Annotations:
-#       class: File
-#       basename: test_proteins.i5_annotations
-#       location: Any
-#       size: Any # To be fixed
+# Note: The checksum is always changed for every executions
+- doc: Test for section 19
+  job: 19-custom-types/custom-types.yml
+  tool: 19-custom-types/custom-types.cwl
+  output:
+    result:
+      class: File
+      basename: rich_sparse_otu_table.hdf5
+      location: Any
+      size: 46992
 
 # Section 20
 # See: Issue #48