bwa-mem example uses ResourceRequest and $resources.cores.

Author: Peter Amstutz

draft-3/draft-3/bwa-mem-job.json

@@ -0,0 +1,25 @@
+{
+    "reference": {
+        "class": "File",
+        "path": "rabix/tests/test-files/chr20.fa",
+        "size": 123,
+        "checksum": "sha1$hash"
+    },
+    "reads": [
+        {
+            "class": "File",
+            "path": "rabix/tests/test-files/example_human_Illumina.pe_1.fastq"
+        },
+        {
+            "class": "File",
+            "path": "rabix/tests/test-files/example_human_Illumina.pe_2.fastq"
+        }
+    ],
+    "min_std_max_min": [
+        1,
+        2,
+        3,
+        4
+    ],
+    "minimum_seed_length": 3
+}

draft-3/draft-3/bwa-mem-job.json

@@ -11,6 +11,9 @@ hints:
     dockerPull: images.sbgenomics.com/rabix/bwa
     dockerImageId: 9d3b9b0359cf
 
+  - class: ResourceRequirement
+    coresMin: 4
+
 inputs:
   - id: "#reference"
     type: File
@@ -43,7 +46,7 @@ baseCommand: ["bwa", "mem"]
 arguments:
   - valueFrom:
       engine: "node-engine.cwl"
-      script: "$job.allocatedResources.cpu"
+      script: "$resources.cores"
     position: 1
     prefix: "-t"