Merge pull request #99 from common-workflow-language/reqs-in-jobdocs

cwl:requirements support in job input documents

Author: mr-c

cwltool/main.py

@@ -174,6 +174,16 @@ def output_callback(out, processStatus):
     else:
         kwargs["outdir"] = tempfile.mkdtemp()
 
+    jobReqs = None
+    if "cwl:requirements" in job_order_object:
+        jobReqs = job_order_object["cwl:requirements"]
+    elif ("cwl:defaults" in t.metadata and "cwl:requirements" in
+            t.metadata["cwl:defaults"]):
+        jobReqs = t.metadata["cwl:defaults"]["cwl:requirements"]
+    if jobReqs:
+        for req in jobReqs:
+            t.requirements.append(req)
+
     jobiter = t.job(job_order_object,
                     output_callback,
                     **kwargs)

tests/echo-cwlrun-job.yaml

@@ -0,0 +1,6 @@
+cwl:tool: echo.cwl
+cwl:requirements:
+ - class: DockerRequirement
+   dockerPull: debian
+
+inp: "Hoopla!"

tests/echo-job.yaml

@@ -0,0 +1,5 @@
+cwl:requirements:
+ - class: DockerRequirement
+   dockerPull: debian
+
+inp: "Howdy!"