Merge pull request #29 from common-workflow-language/20190124_v1.0_refresh

refresh conformance tests from v1.0.x

Author: tetron

conformance_tests.yaml

@@ -0,0 +1,25 @@
+cwlVersion: v1.1.0-dev1
+class: CommandLineTool
+inputs:
+  first:
+    type:
+      type: record
+      fields:
+        species:
+            - type: enum
+              symbols: [homo_sapiens, mus_musculus]
+            - "null"
+  second:
+    type:
+      - "null"
+      - type: enum
+        symbols: [homo_sapiens, mus_musculus]
+baseCommand: echo
+arguments:
+  - prefix: first
+    valueFrom: $(inputs.first.species)
+  - prefix: second
+    valueFrom: $(inputs.second)
+outputs:
+  result: stdout
+

tests/anon_enum_inside_array.cwl

@@ -0,0 +1,3 @@
+first:
+  species: mus_musculus
+second: homo_sapiens

tests/anon_enum_inside_array.yml

@@ -0,0 +1,27 @@
+cwlVersion: v1.1.0-dev1
+class: CommandLineTool
+requirements:
+  SchemaDefRequirement:
+    types: 
+      - name: vcf2maf_params
+        type: record
+        fields:
+          species:
+              - "null"
+              - type: enum
+                symbols: [homo_sapiens, mus_musculus]
+          ncbi_build:
+              - "null"
+              - type: enum
+                symbols: [GRCh37, GRCh38, GRCm38]
+inputs:
+  first: vcf2maf_params
+baseCommand: echo
+arguments:
+  - prefix: species
+    valueFrom: $(inputs.first.species)
+  - prefix: ncbi_build
+    valueFrom: $(inputs.first.ncbi_build)
+outputs:
+  result: stdout
+

tests/anon_enum_inside_array_inside_schemadef.cwl

@@ -0,0 +1,4 @@
+first:  # "vcf2maf_params" record type.
+    species: homo_sapiens  # enum; valid values: "homo_sapiens", "mus_musculus" (optional)
+    ncbi_build: GRCh37  # enum; valid values: "GRCh37", "GRCh38", "GRCm38" (optional)
+

tests/anon_enum_inside_array_inside_schemadef.yml

@@ -1,4 +1,4 @@
-cwlVersion: v1.0
+cwlVersion: v1.1.0-dev1
 tool:
   class: File
   path: echo-tool.cwl  # could have been any file, this isn't a secret CWL feature :-)

tests/basename-fields-job.yml

@@ -0,0 +1,6 @@
+dir1:
+  class: Directory
+  basename: cwl
+  listing:
+   - class: File
+     path: hello.txt

tests/cat-from-dir-job.yaml

@@ -0,0 +1,7 @@
+dir1:
+  class: Directory
+  basename: cwl
+  listing:
+   - class: File
+     basename: literal.txt
+     contents: "I'm a File literal; howdy!"

tests/cat-from-dir-with-literal-file.yaml

@@ -0,0 +1,15 @@
+#!/usr/bin/env cwl-runner
+
+class: CommandLineTool
+cwlVersion: v1.1.0-dev1
+
+inputs:
+  dir1: Directory
+
+outputs:
+  output:
+    type: stdout
+
+baseCommand: [cat]
+
+stdin: $(inputs.dir1.listing[0].path)

tests/cat-from-dir.cwl

@@ -0,0 +1,14 @@
+#!/usr/bin/env cwl-runner
+class: CommandLineTool
+cwlVersion: v1.1.0-dev1
+inputs:
+  dir1:
+    type: Directory
+    inputBinding:
+      valueFrom: $(self.listing[0].path)
+outputs:
+  output_file:
+    type: File
+    outputBinding: {glob: output.txt}
+baseCommand: cat
+stdout: output.txt