Merge branch 'master' into add-fromwdl-to-janisdk

Author: illusional

README.md

@@ -15,8 +15,8 @@ Documentation is available here: https://janis.readthedocs.io/
 
 
 Janis gives you an API to build computational workflows and will generate
-a workflow description in CWL and WDL. By using Janis, you get type-safety,
-portability and reproducibility across all of your execution environments.
+a workflow description in CWL (v1.2) and WDL (version development). By using Janis, 
+you get type-safety, portability and reproducibility across all of your execution environments.
 
 
 Janis requires a Python installation > 3.6, and can be installed through PIP 

docs/index.rst

@@ -54,8 +54,8 @@ Janis requires a Python installation > 3.6, and can be installed through PIP
 
 There are two ways to use Janis:
 
-- Build workflows (and translate to CWL / WDL)
-- Run tools or workflows with CWLTool or Cromwell
+- Build workflows (and translate to CWL (v1.2) / WDL (version development) / Nextflow (in-progress))
+- Run tools or workflows with CWLTool, Cromwell, or Nextflow (in progress)
 
 
 Example Workflow

docs/references/faq.md

@@ -47,7 +47,7 @@ If you're still having trouble, use `janis spider --trace mytool` to give you an
 - **Can a `janis.ToolInput` be marked as streamable?**
 
     Currently there's no support to mark ToolInput's as `streamable`. Although the
-    [`CWL specification`](https://www.commonwl.org/v1.1/CommandLineTool.html#CommandInputParameter).
+    [`CWL specification`](https://www.commonwl.org/v1.2/CommandLineTool.html#CommandInputParameter).
     does support marking inputs as streamable, WDL does not and, there is 
     [no engine support](https://github.com/broadinstitute/cromwell/issues/3454#issuecomment-455367417). 
 
@@ -150,4 +150,4 @@ If you're still having trouble, use `janis spider --trace mytool` to give you an
     You can override the container being used by specifying a `container-override`, there are two ways to do this:
 
     - CLI with the syntax: `janis [translate|run] --container-override 'MyTool=myorganisation/mytool:0.10.0' mytool`
-    - API: include container override dictionary: `mytool.translate("wdl", container_override={"mytool": "myorganisation/mytool:0.10.0"})`, the dictionary has structure: `{toolId: container}`. The toolId can be an asterisk `*` to override all tools' containers.
+    - API: include container override dictionary: `mytool.translate("wdl", container_override={"mytool": "myorganisation/mytool:0.10.0"})`, the dictionary has structure: `{toolId: container}`. The toolId can be an asterisk `*` to override all tools' containers.

janis/__meta__.py

@@ -1,4 +1,4 @@
-__version__ = "v0.11.4"
+__version__ = "v0.11.6"
 
 GITHUB_URL = "https://github.com/PMCC-BioinformaticsCore/janis"
 DOCS_URL = "https://janis.readthedocs.io/en/latest/"

janisdk/fromwdl/__init__.py

@@ -12,7 +12,7 @@ def add_fromwdl_args(parser):
     parser.add_argument("wdlfile", help="The path to the WDL file")
 
     parser.add_argument(
-        "translation", default="janis", choices=["wdl", "wdl", "janis"], nargs="?"
+        "translation", default="janis", choices=["cwl", "wdl", "janis"], nargs="?"
     )
 
     return parser

setup.py

@@ -4,11 +4,11 @@
 DESCRIPTION = "Contains classes and helpers to build a workflow, and provide options to convert to CWL / WDL"
 
 JANIS_CORE_VERSION = "v0.11.5"
-JANIS_ASSISTANT_VERSION = "v0.11.7"
-JANIS_UNIX_VERSION = "v0.11.0"
-JANIS_BIOINFORMATICS_VERSION = "v0.11.1"
-JANIS_PIPELINES_VERSION = "v0.11.3"
-JANIS_TEMPLATES_VERSION = "v0.11.3"
+JANIS_ASSISTANT_VERSION = "v0.11.9"
+JANIS_UNIX_VERSION = "v0.11.2"
+JANIS_BIOINFORMATICS_VERSION = "v0.11.3"
+JANIS_PIPELINES_VERSION = "v0.11.5"
+JANIS_TEMPLATES_VERSION = "v0.12.0"
 
 
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