Merge branch 'master' into inherited-requirements

Author: Kaushik Ghose

CommandLineTool.yml

@@ -50,6 +50,7 @@ $graph:
 
       ## Changelog
 
+        * Clarify behavior around `ENTRYPOINT` and `CMD` in containers
         * Clarify documentation around `valueFrom` and `null` inputs.
         * Default values for some fields are now expressed in the schema.
         * When defining record types with `CommandInputRecordSchema`, fields of
@@ -701,8 +702,9 @@ $graph:
   extends: ProcessRequirement
   doc: |
     Indicates that a workflow component should be run in a
-    [Docker](http://docker.com) container, and specifies how to fetch or build
-    the image.
+    [Docker](http://docker.com) or Docker-compatible (such as
+    [Singularity](https://www.sylabs.io/) and [udocker](https://github.com/indigo-dc/udocker)) container environment and
+    specifies how to fetch or build the image.
 
     If a CommandLineTool lists `DockerRequirement` under
     `hints` (or `requirements`), it may (or must) be run in the specified Docker
@@ -727,6 +729,22 @@ $graph:
     generated command line represents a valid command within the runtime
     environment of the container.
 
+    A container image may specify an
+    [ENTRYPOINT](https://docs.docker.com/engine/reference/builder/#entrypoint)
+    and/or
+    [CMD](https://docs.docker.com/engine/reference/builder/#cmd).
+    Command line arguments will be appended after all elements of
+    ENTRYPOINT, and will override all elements specified using CMD (in
+    other words, CMD is only used when the CommandLineTool definition
+    produces an empty command line).
+
+    Use of implicit ENTRYPOINT or CMD are discouraged due to reproducibility
+    concerns of the implicit hidden execution point (For further discussion, see 
+    [https://doi.org/10.12688/f1000research.15140.1](https://doi.org/10.12688/f1000research.15140.1)). Portable 
+    CommandLineTool wrappers in which use of a container is optional must not rely on ENTRYPOINT or CMD.  
+    CommandLineTools which do rely on ENTRYPOINT or CMD must list `DockerRequirement` in the
+    `requirements` section.
+
     ## Interaction with other requirements
 
     If [EnvVarRequirement](#EnvVarRequirement) is specified alongside a

README.md

@@ -2,6 +2,8 @@ Hello!
 
 This repo represent the current working proposal for v1.1 of the Common Workflow Language standard.
 
+Proposed changes that aren't yet implemented are tracked at https://github.com/common-workflow-language/common-workflow-language/milestone/6
+
 You can render this using https://github.com/common-workflow-language/cwl-website/blob/master/website.sh
 
 The current rendering is at https://www.commonwl.org/v1.1.0-dev1/

Workflow.yml

@@ -49,6 +49,7 @@ $graph:
       ## Changelog
 
         * Clarify how Requirements are inherited by step processes
+        * Document explicitly that CWL allows pass-through of workflow inputs to outputs
         * Default values for some fields are now expressed in the schema
         * When defining record types, fields of type `File` may now include
           `format`, `secondaryFiles`, and `streamable`.
@@ -184,8 +185,9 @@ $graph:
   docParent: "#Workflow"
   doc: |
     Describe an output parameter of a workflow.  The parameter must be
-    connected to one or more parameters defined in the workflow that will
-    provide the value of the output parameter.
+    connected to one or more parameters defined in the workflow that 
+    will provide the value of the output parameter. It is legal to
+    connect a WorkflowInputParameter to a WorkflowOutputParameter.
   fields:
     - name: outputSource
       doc: |

conformance_tests.yaml

@@ -2711,3 +2711,20 @@
             }
         ]
 }
+
+- doc: Test that OutputBinding.glob accepts Directories
+  job: tests/empty.json
+  label: outputbinding_glob_directory
+  tool: tests/glob_directory.cwl
+  output:
+    directories:
+        - basename: "a_dir"
+          class: "Directory"
+          listing: []
+        - basename: "b_dir"
+          class: "Directory"
+          listing: []
+        - basename: "c_dir"
+          class: "Directory"
+          listing: []
+  tags: [ required, command_line_tool ]

tests/glob_directory.cwl

@@ -0,0 +1,10 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.1.0-dev1
+class: CommandLineTool
+
+inputs: []
+baseCommand: [mkdir, a_dir, b_dir, c_dir]
+outputs:
+  directories:
+    type: Directory[]
+    outputBinding: { glob: '[a,b,c]_dir' }