Command line generation tests now work by executing a small script that copies

the command line to the output.  Allows cwl-runner implementations to drop the
--conformance-test code path.

Author: Peter Amstutz

draft-2/conformance_test_draft-2.yaml

@@ -1,63 +1,52 @@
-- args: [bwa, mem, -t, '4', -I, '1,2,3,4', -m, '3', draft-2/rabix/tests/test-files/chr20.fa,
-    draft-2/rabix/tests/test-files/example_human_Illumina.pe_1.fastq, draft-2/rabix/tests/test-files/example_human_Illumina.pe_2.fastq]
+- args:
   job: draft-2/bwa-mem-job.json
-  stdout: output.sam
   tool: draft-2/bwa-mem-tool.cwl
+  output:
+    args: [bwa, mem, -t, '4', -I, '1,2,3,4', -m, '3',
+      chr20.fa,
+      example_human_Illumina.pe_1.fastq,
+      example_human_Illumina.pe_2.fastq]
   doc: General test of command line generation
 
-- args: [bwa, mem, draft-2/rabix/tests/test-files/chr20.fa,
-    "-XXX",
-    "-YYY", draft-2/rabix/tests/test-files/example_human_Illumina.pe_1.fastq,
-    "-YYY", draft-2/rabix/tests/test-files/example_human_Illumina.pe_2.fastq]
+- output:
+    args: [bwa, mem, chr20.fa,
+      "-XXX",
+      "-YYY", example_human_Illumina.pe_1.fastq,
+      "-YYY", example_human_Illumina.pe_2.fastq]
   job: draft-2/bwa-mem-job.json
   tool: draft-2/binding-test.cwl
   doc: Test nested prefixes with arrays
 
-- args: [tmap, mapall, stage1, map1, --min-seq-length, '20', map2, --min-seq-length,
+- output:
+    args: [tmap, mapall, stage1, map1, --min-seq-length, '20', map2, --min-seq-length,
     '20', stage2, map1, --max-seq-length, '20', --min-seq-length, '10', --seed-length,
     '16', map2, --max-seed-hits, '-1', --max-seq-length, '20', --min-seq-length, '10']
   job: draft-2/tmap-job.json
-  stdin: draft-2/reads.fastq
-  stdout: output.sam
   tool: draft-2/tmap-tool.cwl
-  doc: Test nested command line bindings and stdin/stdout redirection
+  doc: Test nested command line bindings
 
-- args: [cat, draft-2/hello.txt]
+- output:
+    args: [cat, hello.txt]
   job: draft-2/cat-job.json
-  tool: draft-2/cat1-tool.cwl
+  tool: draft-2/cat1-testcli.cwl
   doc: Test command line with optional input (missing)
 
-- args: [cat, -n, draft-2/hello.txt]
+- output:
+    args: [cat, -n, hello.txt]
   job: draft-2/cat-n-job.json
-  tool: draft-2/cat1-tool.cwl
+  tool: draft-2/cat1-testcli.cwl
   doc: Test command line with optional input (provided)
 
-- args: [cat]
-  job: draft-2/cat-job.json
-  stdin: draft-2/hello.txt
-  tool: draft-2/cat2-tool.cwl
-  doc: Test command line with stdin redirection
-
-- args: [cat, draft-2/hello.txt]
-  job: draft-2/cat-job.json
-  stdout: output.txt
-  tool: draft-2/cat3-tool.cwl
-  doc: Test command line with stdout redirection
-
-- args: [cat]
-  job: draft-2/cat-job.json
-  stdin: draft-2/hello.txt
-  stdout: output.txt
-  tool: draft-2/cat4-tool.cwl
-  doc: Test command line with stdin and stdout redirection
-
-- args: [cat, foo.txt]
-  createfiles: {foo.txt: 'The file is draft-2/hello.txt
-
-      '}
+- output:
+    "foo": {
+        "checksum": "sha1$63da67422622fbf9251a046d7a34b7ea0fd4fead",
+        "class": "File",
+        "path": "foo.txt",
+        "size": 22
+    }
   job: draft-2/cat-job.json
   tool: draft-2/template-tool.cwl
-  doc: Test CreateFileRequirement ExpressionEngineRequirement.engineConfig features
+  doc: Test CreateFileRequirement ExpressionEngineRequirement.engineConfig feature
 
 - job: draft-2/cat-job.json
   output:

draft-2/draft-2/args.py

@@ -0,0 +1,7 @@
+#!/usr/bin/env python
+import sys
+import json
+import os
+args = [os.path.basename(a) for a in sys.argv[1:]]
+with open("cwl.output.json", "w") as f:
+    json.dump({"args": args}, f)

draft-2/draft-2/binding-test.cwl

@@ -14,6 +14,15 @@ inputs:
       inputBinding: { prefix: "-YYY" }
     inputBinding: { position: 3, prefix: "-XXX" }
 
+  - id: "#args.py"
+    type: File
+    default:
+      class: File
+      path: args.py
+    inputBinding:
+      position: -1
+
 outputs: []
 
-baseCommand: ["bwa", "mem"]
+baseCommand: python
+arguments: ["bwa", "mem"]

draft-2/draft-2/bwa-mem-job.json

@@ -1,18 +1,18 @@
 {
     "reference": {
         "class": "File",
-        "path": "rabix/tests/test-files/chr20.fa",
+        "path": "chr20.fa",
         "size": 123,
         "checksum": "sha1$hash"
     },
     "reads": [
         {
             "class": "File",
-            "path": "rabix/tests/test-files/example_human_Illumina.pe_1.fastq"
+            "path": "example_human_Illumina.pe_1.fastq"
         },
         {
             "class": "File",
-            "path": "rabix/tests/test-files/example_human_Illumina.pe_2.fastq"
+            "path": "example_human_Illumina.pe_2.fastq"
         }
     ],
     "min_std_max_min": [

draft-2/draft-2/bwa-mem-tool.cwl

@@ -4,11 +4,6 @@ class: CommandLineTool
 requirements:
   - import: node-engine.cwl
 
-hints:
-  - class: DockerRequirement
-    dockerPull: images.sbgenomics.com/rabix/bwa
-    dockerImageId: 9d3b9b0359cf
-
 inputs:
   - id: "#reference"
     type: File
@@ -31,14 +26,28 @@ inputs:
       prefix: "-I"
       itemSeparator: ","
 
+  - id: "#args.py"
+    type: File
+    default:
+      class: File
+      path: args.py
+    inputBinding:
+      position: -1
+
 outputs:
   - id: "#sam"
-    type: "File"
+    type: ["null", "File"]
     outputBinding: { "glob": "output.sam" }
+  - id: "#args"
+    type:
+      type: array
+      items: string
 
-baseCommand: ["bwa", "mem"]
+baseCommand: python
 
 arguments:
+  - "bwa"
+  - "mem"
   - valueFrom:
       engine: "node-engine.cwl"
       script: "$job.allocatedResources.cpu"

draft-2/draft-2/cat1-testcli.cwl

@@ -0,0 +1,34 @@
+#!/usr/bin/env cwl-runner
+{
+    "class": "CommandLineTool",
+    "description": "Print the contents of a file to stdout using 'cat' running in a docker container.",
+    "inputs": [
+        {
+            "id": "#file1",
+            "type": "File",
+            "inputBinding": {"position": 1}
+        },
+        {
+            "id": "#numbering",
+            "type": ["null", "boolean"],
+            "inputBinding": {
+                "position": 0,
+                "prefix": "-n"
+            }
+        },
+        {
+        id: "#args.py",
+        type: File,
+        default: {
+          class: File,
+          path: args.py
+        },
+        inputBinding: {
+          position: -1
+        }
+      }
+    ],
+    "outputs": [],
+    "baseCommand": "python",
+    "arguments": ["cat"]
+}

draft-2/draft-2/cat2-tool.cwl

@@ -17,9 +17,14 @@ requirements:
       - filename: foo.txt
         fileContent:
           engine: "#js"
-          script: 't("The file is <%= $job.file1.path %>\n")'
+          script: >
+            t("The file is <%= $job.file1.path.split('/').slice(-1)[0] %>\n")
 inputs:
   - id: "#file1"
     type: File
-outputs: []
+outputs:
+  - id: "#foo"
+    type: File
+    outputBinding:
+      glob: foo.txt
 baseCommand: ["cat", "foo.txt"]

draft-2/draft-2/chr20.fa

@@ -16,15 +16,26 @@
                 "type": "array",
                 "items": "Stage"
             }
+        },
+        {
+        id: "#args.py",
+        type: File,
+        default: {
+          class: File,
+          path: args.py
+        },
+        inputBinding: {
+          position: -1
         }
+      }
     ],
     "outputs": [
         {
             "id": "#sam",
             "outputBinding": {
                 "glob": "output.sam"
             },
-            "type": "File"
+            "type": ["null", "File"]
         }
     ],
     "requirements": [
@@ -233,10 +244,6 @@
             ]
         }
     ]}],
-    "baseCommand": ["tmap", "mapall"],
-    "stdin": {
-      "engine": "cwl:JsonPointer",
-      "script": "job/reads/path"
-      },
-    "stdout": "output.sam"
+    "baseCommand": "python",
+    "arguments": ["tmap", "mapall"]
 }