Update user guide for v1.0

Author: Peter Amstutz

run_test.sh

@@ -11,7 +11,7 @@ Options:
   -l    List tests
 EOF
 
-DRAFT=draft-3
+DRAFT=v1.0
 TEST_N=""
 RUNNER=cwl-runner
 PLATFORM=$(uname -s)

v1.0/UserGuide.yml

@@ -41,11 +41,11 @@
       What's going on here?  Let's break it down:
 
       ```
-      cwlVersion: cwl:draft-3
+      cwlVersion: v1.0
       class: CommandLineTool
       ```
 
-      The 'cwlVersion` field indicates the version of the CWL spec used by the
+      The `cwlVersion` field indicates the version of the CWL spec used by the
       document.  The `class` field indicates this document describes a command
       line tool.
 
@@ -58,7 +58,7 @@
 
       ```
       inputs:
-        - id: message
+        message:
           type: string
           inputBinding:
             position: 1
@@ -123,7 +123,7 @@
       line.  Let's look at each example in detail.
 
       ```
-      - id: example_flag
+      example_flag:
         type: boolean
         inputBinding:
           position: 1
@@ -135,7 +135,7 @@
       command line.  If false, no flag is added.
 
       ```
-      - id: example_string
+      example_string:
         type: string
         inputBinding:
           position: 3
@@ -148,7 +148,7 @@
       rendered as `--example-string hello`.
 
       ```
-      - id: example_int
+      example_int:
         type: int
         inputBinding:
           position: 2
@@ -163,19 +163,17 @@
 
 
       ```
-      - id: example_file
-        type: ["null", File]
+      example_file:
+        type: File?
         inputBinding:
           prefix: --file=
           separate: false
           position: 4
       ```
 
       File types appear on the command line as the path to the file.  When the
-      parameter type is a list, this indicates several alternate types are
-      valid for this parameter.  The most common use is to provide "null" as an
-      alternate parameter type, which indicates that the parameter is optional.
-      In the example above, this is rendered as
+      parameter type ends with a question mark `?` it indicates that the
+      parameter is optional.  In the example above, this is rendered as
       `--file=/home/example/whale.txt`.  However, if the "example_file"
       parameter were not provided in the input, nothing would appear on the
       command line.
@@ -228,7 +226,7 @@
       Final process status is success
       {
       "example_out": {
-        "path": "hello.txt",
+        "location": "hello.txt",
         "size": 13,
         "class": "File",
         "checksum": "sha1$47a013e660d408619d894b20806b1d5086aab03b"
@@ -255,8 +253,8 @@
       ## Capturing a tool's standard output stream
 
       To capture a tool's standard output stream, add the `stdout` field with
-      the name of the file where the output stream should go.  Then use `glob`
-      on `outputBinding` to return the file.
+      the name of the file where the output stream should go.  Then add `type:
+      stdout` on the corresponding output parameter.
 
       *stdout.cwl*
       ```
@@ -279,7 +277,7 @@
       Final process status is success
       {
       "output": {
-        "path": "output.txt",
+        "location": "output.txt",
         "size": 13,
         "class": "File",
         "checksum": "sha1$47a013e660d408619d894b20806b1d5086aab03b"
@@ -319,7 +317,7 @@
       Final process status is success
       {
       "example_out": {
-        "path": "goodbye.txt",
+        "location": "goodbye.txt",
         "size": 24,
         "class": "File",
         "checksum": "sha1$dd0a4c4c49ba43004d6611771972b6cf969c1c01"
@@ -332,7 +330,7 @@
 
       ```
       outputs:
-        - id: example_out
+        example_out:
           type: File
           outputBinding:
             glob: $(inputs.extractfile)
@@ -427,12 +425,28 @@
       ```
       $ echo "public class Hello {}" > Hello.java
       $ cwl-runner arguments.cwl arguments-job.yml
-      [job 140051188854928] /home/example$ docker run -i --volume=/home/example/Hello.java:/var/lib/cwl/job710906416_example/Hello.java:ro --volume=/home/example:/var/spool/cwl:rw --volume=/tmp/tmpdlQDWi:/tmp:rw --workdir=/var/spool/cwl --read-only=true --net=none --user=1001 --rm --env=TMPDIR=/tmp java:7 javac -d /var/spool/cwl /var/lib/cwl/job710906416_examples/Hello.java
+      [job arguments.cwl] /tmp/tmpwYALo1$ docker \
+       run \
+       -i \
+       --volume=/home/peter/work/common-workflow-language/v1.0/examples/Hello.java:/var/lib/cwl/stg8939ac04-7443-4990-a518-1855b2322141/Hello.java:ro \
+       --volume=/tmp/tmpwYALo1:/var/spool/cwl:rw \
+       --volume=/tmp/tmpptIAJ8:/tmp:rw \
+       --workdir=/var/spool/cwl \
+       --read-only=true \
+       --user=1001 \
+       --rm \
+       --env=TMPDIR=/tmp \
+       --env=HOME=/var/spool/cwl \
+       java:7 \
+       javac \
+       -d \
+       /var/spool/cwl \
+       /var/lib/cwl/stg8939ac04-7443-4990-a518-1855b2322141/Hello.java
       Final process status is success
       {
         "classfile": {
           "size": 416,
-          "path": "/home/example/Hello.class",
+          "location": "/home/example/Hello.class",
           "checksum": "sha1$2f7ac33c1f3aac3f1fec7b936b6562422c85b38a",
           "class": "File"
         }
@@ -444,9 +458,7 @@
       command line that isn't tied to a specific input parameter.
 
       ```
-      arguments:
-        - prefix: "-d"
-          valueFrom: $(runtime.outdir)
+      arguments: ["-d", $(runtime.outdir)]
       ```
 
       This example references a runtime parameter.  Runtime parameters
@@ -527,13 +539,13 @@
         "output": [
           {
             "size": 0,
-            "path": "/home/peter/work/common-workflow-language/draft-3/examples/foo.txt",
+            "location": "/home/peter/work/common-workflow-language/draft-3/examples/foo.txt",
             "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
             "class": "File"
           },
           {
             "size": 0,
-            "path": "/home/peter/work/common-workflow-language/draft-3/examples/baz.txt",
+            "location": "/home/peter/work/common-workflow-language/draft-3/examples/baz.txt",
             "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
             "class": "File"
           }
@@ -726,7 +738,7 @@
       {
       "classfile": {
         "size": 416,
-        "path": "/home/example/Hello.class",
+        "location": "/home/example/Hello.class",
         "checksum": "sha1$2f7ac33c1f3aac3f1fec7b936b6562422c85b38a",
         "class": "File"
         }
@@ -759,6 +771,7 @@
       command line:
 
       ```
+      $ echo "public class Hello {}" > Hello.java && tar -cvf hello.tar Hello.java
       $ cwl-runner 1st-workflow.cwl 1st-workflow-job.yml
       [job untar] /tmp/tmp94qFiM$ tar xf /home/example/hello.tar Hello.java
       [step untar] completion status is success
@@ -768,8 +781,8 @@
       Final process status is success
       {
         "classout": {
-          "path": "/home/example/Hello.class",
-          "checksum": "sha1$2f7ac33c1f3aac3f1fec7b936b6562422c85b38a",
+          "location": "/home/example/Hello.class",
+          "checksum": "sha1$e68df795c0686e9aa1a1195536bd900f5f417b18",
           "class": "File",
           "size": 416
         }
@@ -779,7 +792,7 @@
       What's going on here?  Let's break it down:
 
       ```
-      cwlVersion: cwl:draft-3
+      cwlVersion: v1.0
       class: Workflow
       ```
 
@@ -789,10 +802,8 @@
 
       ```
       inputs:
-        - id: inp
-          type: File
-        - id: ex
-          type: string
+        inp: File
+        ex: string
       ```
 
       The `inputs` section describes the inputs of the workflow.  This is a
@@ -802,9 +813,9 @@
 
       ```
       outputs:
-        - id: classout
+        classout:
           type: File
-          source: "#compile/classfile"
+          outputSource: compile/classfile
       ```
 
       The `outputs` section describes the outputs of the workflow.  This is a
@@ -814,15 +825,12 @@
 
       ```
       steps:
-        - id: untar
+        untar:
           run: tar-param.cwl
-          inputs:
-            - id: tarfile
-              source: "#inp"
-            - id: extractfile
-              source: "#ex"
-          outputs:
-            - id: example_out
+          in:
+            tarfile: inp
+            extractfile: ex
+          outputs: [example_out]
       ```
 
       The `steps` section describes the actual steps of the workflow.  In this
@@ -839,25 +847,23 @@
       `example_out`.
 
       The `inputs` section of the workflow step connects these two input
-      parameters to the inputs of the workflow, `#inp` and `#ex` using
+      parameters to the inputs of the workflow, `inp` and `ex` using
       `source`.  This means that when the workflow step is executed, the values
-      assigned to `#inp` and `#ex` will be used for the parameters `tarfile`
+      assigned to `inp` and `ex` will be used for the parameters `tarfile`
       and `extractfile` in order to run the tool.
 
       The `outputs` section of the workflow step lists the output parameters
       that are expected from the tool.
 
       ```
-        - id: compile
+        compile:
           run: arguments.cwl
-          inputs:
-            - id: src
-              source: "#untar/example_out"
-          outputs:
-            - id: classfile
+          in:
+            src: untar/example_out
+          outputs: [classfile]
       ```
 
       The second step `compile` depends on the results from the first step by
       connecting the input parameter `src` to the output parameter of `untar`
-      using `#untar/example_out`.  The output of this step `classfile` is
+      using `untar/example_out`.  The output of this step `classfile` is
       connected to the `outputs` section for the Workflow, described above.

v1.0/conformance_test_v1.0.yaml

@@ -789,3 +789,15 @@
       size: 18
   tool: v1.0/cat3-tool.cwl
   doc: Test file literal as input
+
+- job: examples/arguments-job.yml
+  output: {
+    "classfile": {
+        "checksum": "sha1$2f7ac33c1f3aac3f1fec7b936b6562422c85b38a",
+        "location": "Hello.class",
+        "class": "File",
+        "size": 416
+    }
+  }
+  tool: examples/linkfile.cwl
+  doc: The expression in InitialWorkDir listing

v1.0/examples/1st-workflow.cwl

@@ -7,18 +7,18 @@ inputs:
 outputs:
   classout:
     type: File
-    outputSource: "#compile/classfile"
+    outputSource: compile/classfile
 
 steps:
   untar:
     run: tar-param.cwl
-    inputs:
+    in:
       tarfile: inp
       extractfile: ex
-    outputs: [example_out]
+    out: [example_out]
 
   compile:
     run: arguments.cwl
-    inputs:
+    in:
       src: untar/example_out
-    outputs: [classfile]
+    out: [classfile]

v1.0/examples/Hello.java

@@ -1,7 +1 @@
-public class Hello
-{
-    public static void main(String[] args)
-    {
-        System.out.println("Hello world!");
-    }
-}
+public class Hello {}

v1.0/examples/array-inputs.cwl

@@ -2,9 +2,7 @@ cwlVersion: v1.0
 class: CommandLineTool
 inputs:
   filesA:
-    type:
-      type: array
-      items: string
+    type: string[]
     inputBinding:
       prefix: -A
       position: 1
@@ -20,9 +18,7 @@ inputs:
       position: 2
 
   filesC:
-    type:
-      type: array
-      items: string
+    type: string[]
     inputBinding:
       prefix: -C=
       itemSeparator: ","

v1.0/examples/createfile.cwl

@@ -3,10 +3,11 @@ cwlVersion: v1.0
 baseCommand: ["cat", "example.conf"]
 
 requirements:
-  InitialWorkDirRequirirement:
+  InitialWorkDirRequirement:
     listing:
-      example.conf: |
-        CONFIGVAR=$(inputs.message)
+      - entryname: example.conf
+        entry: |
+          CONFIGVAR=$(inputs.message)
 
 inputs:
   message: string