Draft: Scientific wf domain specific language

A simple workflow language with FireWorks as backend.

• Python functions
  • function names, kwargs
  • dataflow: input and output data
• Shell scripts
  • script as a string
  • managing stdin, stdout, stderr
  • manage files (stage-in, stage-out)

solving issue #17 (closed)

workflows/example.wf

+// A test program in the simple workflow language
+
+workflow: Test "Example workflow"
+
+node: Node1
+  tasks: Script1
+  files_out: fwtest1
+
+node: Node2
+  tasks: Script2
+  parents: Node1
+  files_in: fwtest1
+  files_out: fw2
+
+node: Node3
+  tasks: Script3
+  parents: Node2
+  files_in: fw2
+
+node: Node4
+  tasks: Exponent
+  parents: Node3
+
+node: Node5
+  tasks: Script4
+  parents: Node4
+
+node: Node6
+  tasks: Script5
+  parents: Node5
+
+script: Script1
+  script: 'echo "This is the first FireWork" > test1'
+
+script: Script2
+  script: 'gzip hello'
+
+script: Script3
+  script: 'cat fwtest.2'
+
+script: Script4
+  script: 'echo "Kip is an intern."'
+  stdout_file: 'intern.txt'
+  stderr_file: 'error.txt'
+
+script: Script5
+  script: 'cat -t'
+  stdin_file: 'intern.txt'
+  stdout_file: 'output.txt'
+  stderr_file: 'error.txt'
+
+pytask: Logarithm
+  func: "math.log"
+  inputs: bar1
+  outputs: foobar
+
+pytask: Exponent
+  func: "math.exp"
+  outputs: blah3
+  inputs: bar4
+  
+data: Blah []
+data: bar4 0
+data: bar1 4.0
+
+odata: blah3
+odata: fooo2
+odata: foobar
+
+filesout: fwtest1 "test1"
+filesout: fw2 "hello.gz"
+
+filesin: fwtest1 "hello"
+filesin: fw2 "fwtest.2"
+
+query:
+  nodes: queryid
+
+nodeinfo: queryid
+  nodedetail: [1234, 123]
\ No newline at end of file