Merge pull request #65 from PMCC-BioinformaticsCore/release-v0.12.0

Release v0.12.0

.github/workflows/unit_tests.yml

@@ -1,6 +1,6 @@
 name: Unit Tests
 
-on: [push]
+on: [push, pull_request]
 
 jobs:
   build:
@@ -23,4 +23,4 @@ jobs:
     - name: Test with nosetests
       run: |
         nosetests -w janis_assistant --with-coverage --cover-package=janis_assistant
-    - uses: codecov/codecov-action@v1
+    - uses: codecov/codecov-action@v1

janis_assistant/cli.py

@@ -94,7 +94,7 @@ def process_args(sysargs=None):
     )
     add_translate_args(
         subparsers.add_parser(
-            "translate", help="Translate a janis workflow to CWL or WDL"
+            "translate", help="Translate a janis workflow to CWL, WDL, or Nextflow"
         )
     )
     add_inputs_args(

janis_assistant/data/models/preparedjob.py

@@ -9,6 +9,7 @@
 from janis_assistant.management.configuration import (
     parse_if_dict,
     JanisConfigurationCromwell,
+    JanisConfigurationNextflow,
     JanisConfigurationTemplate,
     JanisConfigurationNotifications,
     JanisConfigurationEnvironment,
@@ -66,6 +67,7 @@ def __init__(
         container_type: str = None,
         workflow_reference: str = None,
         post_run_script: str = None,
+        nextflow: JanisConfigurationNextflow = None
     ):
         """
 
@@ -116,6 +118,10 @@ def __init__(
             "cromwell",
             skip_if_empty=not requires_cromwell_config,
         )
+        requires_nextflow_config = self.engine == EngineType.nextflow
+        self.nextflow: JanisConfigurationNextflow = parse_if_dict(
+            JanisConfigurationNextflow, nextflow or {}, "nextflow", skip_if_empty=not requires_nextflow_config
+        )
         self.template: JanisConfigurationTemplate = parse_if_dict(
             JanisConfigurationTemplate, template or {}, "template", skip_if_empty=False
         )

janis_assistant/data/models/run.py

@@ -268,7 +268,7 @@ def format(self, **kwargs):
             errors.extend(r.error for r in self.runs if r.error)
 
             rstatuses = ", ".join(
-                str(r.status.to_string()) for r in self.runs if r.status
+                str(r.status) for r in self.runs if r.status
             )
 
         statuses = self.status.to_string() if self.status else rstatuses

janis_assistant/engines/__init__.py

@@ -4,6 +4,7 @@
 from .cromwell import Cromwell, CromwellConfiguration
 from .enginetypes import EngineType
 from .cwltool.main import CWLTool
+from .nextflow.main import Nextflow
 from .engine import Engine
 from janis_core import SupportedTranslation
 
@@ -15,6 +16,9 @@ def get_ideal_specification_for_engine(eng: Engine):
     elif isinstance(eng, Toil):
         return SupportedTranslation.CWL
 
+    elif isinstance(eng, Nextflow):
+        return SupportedTranslation.Nextflow
+
     return SupportedTranslation.CWL
 
 
@@ -26,5 +30,7 @@ def get_engine_type(engtype: Union[str, EngineType]):
         return CWLTool
     elif engid == EngineType.toil.value:
         return Toil
+    elif engid == EngineType.nextflow.value:
+        return Nextflow
 
     raise Exception("Couldn't recognise engine type ")

janis_assistant/engines/engine.py

@@ -64,7 +64,16 @@ def terminate_task(self, identifier) -> TaskStatus:
 
     @abstractmethod
     def metadata(self, identifier) -> RunModel:
-        pass
+        return RunModel(
+            id_=identifier,
+            engine_id=identifier,
+            execution_dir=None,
+            submission_id=None,
+            name=identifier,
+            status=self.taskmeta.get("status"),
+            jobs=list(self.taskmeta.get("jobs", {}).values()),
+            error=self.taskmeta.get("error"),
+        )
 
     keys_to_ignore = {"progress_callbacks"}
 

janis_assistant/engines/enginetypes.py

@@ -5,10 +5,11 @@ class EngineType(Enum):
     cromwell = "cromwell"
     cwltool = "cwltool"
     toil = "toil"
+    nextflow = "nextflow"
 
     def __str__(self):
         return self.value
 
     @staticmethod
     def engines():
-        return [EngineType.cwltool.value, EngineType.cromwell.value]
+        return [EngineType.cwltool.value, EngineType.cromwell.value, EngineType.nextflow.value]