Merge branch '1.2.1_proposed' into fail_expressiontool

.github/config/spellcheck.yml

@@ -0,0 +1,21 @@
+matrix:
+- name: Markdown
+  aspell:
+    lang: en
+    ignore-case: true
+  dictionary:
+    encoding: utf-8
+    wordlists:
+      - .github/config/wordlist.txt
+  pipeline:
+  - pyspelling.filters.markdown:
+  - pyspelling.filters.html:
+      comments: true
+      attributes:
+      - title
+      - alt
+      ignores:
+      - :matches(code, pre)
+  sources:
+  - '**/*.md'
+  default_encoding: utf-8

.github/config/wordlist.txt

@@ -0,0 +1,155 @@
+acyclic
+amstutz
+arvados
+auditability
+avro
+backchannel
+backrub
+basedir
+bnf
+bogdan
+checkpoint
+checkpointing
+chilton
+cisphobia
+classname
+commandlinetool
+commandlinetools
+commonwl
+complextype
+coreutils
+ctbrown
+curii
+curoverse
+cwl
+cwltest
+cwltool
+cwlversion
+cyclic
+dataflow
+dev
+dockerrequirement
+doubleq
+dsl
+dusenbery
+edu
+eg
+envvarrequirement
+expressionlib
+expressiontool
+expressiontools
+filesystem
+freedesktop
+gavrilovic
+ghose
+gitter
+gmail
+hervé
+https
+ietf
+implementer
+implementers
+implementor
+implementors
+initialworkdirrequirement
+initialworkdirrequirements
+inlinejavascriptrequirement
+inplaceupdaterequirement
+inputparameter
+institut
+invocab
+iri
+jmchilton
+json
+junit
+kaushik
+ld
+lexicographically
+linkmerge
+lookahead
+maccallum
+macos
+mebibyte
+mebibytes
+ménager
+metaschema
+misgendering
+mrc
+multipleinputfeaturerequirement
+multithreaded
+namespace
+namespaces
+nebojsa
+nebojša
+nekrutenko
+networkaccess
+neuro
+onlinepubs
+opengroup
+orcid
+osx
+outputsource
+petermac
+pickvalue
+posix
+pre
+preprocess
+preprocessed
+preprocessing
+psu
+publically
+pvanheus
+rdf
+recurse
+repo
+reproducibility
+resourcerequirement
+routable
+runtime
+sbgenomics
+scatterfeaturerequirement
+schemadefrequirement
+schemaorg
+schemas
+secondaryfiles
+secondaryfilesdsl
+shellcommandrequirement
+singleq
+softwarepackage
+softwarerequirement
+soiland
+stepinputexpressionrequirement
+stian
+subdirectory
+subprocess
+subprocesses
+subscope
+subscoped
+subshell
+substep
+substring
+substrings
+subtype
+subtypes
+subworkflow
+subworkflowrequirement
+superset
+svg
+tijanic
+tijanić
+toc
+tooltimelimit
+transcode
+txt
+uc
+ucdavis
+untrusted
+uri
+utf
+vandewege
+virtualenv
+walkthrough
+wdl
+whitespace
+xdg
+yaml

.github/workflows/spellcheck.yml

@@ -0,0 +1,21 @@
+name: Spellcheck Action
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main, 1.2.1_proposed ]
+  workflow_dispatch:
+
+jobs:
+  build:
+    # https://github.com/marketplace/actions/github-spellcheck-action
+    # To run locally, `pip install pyspelling`, followed by
+    # `pyspelling -c .github/config/spellcheck.yml`.
+    name: Spellcheck
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@master
+      - uses: rojopolis/[email protected]
+        name: Spellcheck
+        with:
+          config_path: .github/config/spellcheck.yml

CODE_OF_CONDUCT.md

@@ -43,7 +43,7 @@ except as necessary to protect vulnerable people from intentional abuse.
  - Publication of non-harassing private communication.
 
 The CWL Project prioritizes marginalized people’s safety over privileged
-people’s comfort. The CWL Leadeship Team will not act on complaints regarding:
+people’s comfort. The CWL Leadership Team will not act on complaints regarding:
 
  - ‘Reverse’ -isms, including ‘reverse racism,’ ‘reverse sexism,’ and ‘cisphobia’
  - Reasonable communication of boundaries, such as “leave me alone,” “go away,” or

CONFORMANCE_TESTS.md

@@ -184,7 +184,7 @@ Likewise, please do not test the `path` for `class: File` and `class: Directory`
 
 To add a new conformance test:
 1. Ensure the CWL document you have tests the desired feature or aspect.
-2. All `CommandLineTool`s need a software container (via `DockerRequirement`) for better reproducibility, preferrably under `hints`.
+2. All `CommandLineTool`s need a software container (via `DockerRequirement`) for better reproducibility, preferably under `hints`.
      Please limit your container usage to the following: 
      - `dockerPull: docker.io/alpine:latest`
      - `dockerPull: docker.io/bash:4.4`

CommandLineTool.yml

@@ -567,6 +567,10 @@ $graph:
     stdout: random_stdout_filenameABCDEFG
     ```
 
+    If the `CommandLineTool` contains logically chained commands
+    (e.g. `echo a && echo b`) `stdout` must include the output of
+    every command.
+
 
 - name: stderr
   type: enum
@@ -700,6 +704,10 @@ $graph:
         Capture the command's standard output stream to a file written to
         the designated output directory.
 
+        If the `CommandLineTool` contains logically chained commands
+        (e.g. `echo a && echo b`) `stdout` must include the output of
+        every command.
+
         If `stdout` is a string, it specifies the file name to use.
 
         If `stdout` is an expression, the expression is evaluated and must
@@ -1017,8 +1025,8 @@ $graph:
 
     Normally files are staged within the designated output directory.
     However, when running inside containers, files may be staged at
-    arbitrary locations, see discussion for `Dirent.entryname`.
-    Together with `DockerRequirement.dockerOutputDirectory` this it
+    arbitrary locations, see discussion for [`Dirent.entryname`](#Dirent).
+    Together with `DockerRequirement.dockerOutputDirectory` it is
     possible to control the locations of both input and output files
     when running in containers.
   fields:
@@ -1105,8 +1113,8 @@ $graph:
   extends: ProcessRequirement
   doc: |
     Modify the behavior of CommandLineTool to generate a single string
-    containing a shell command line.  Each item in the argument list must be
-    joined into a string separated by single spaces and quoted to prevent
+    containing a shell command line.  Each item in the `arguments` list must
+    be joined into a string separated by single spaces and quoted to prevent
     intepretation by the shell, unless `CommandLineBinding` for that argument
     contains `shellQuote: false`.  If `shellQuote: false` is specified, the
     argument is joined into the command string without quoting, which allows

README.md

@@ -4,6 +4,6 @@ This repo holds the development version of CWL v1.2.1; see https://github.com/co
 
 See https://github.com/common-workflow-language/cwl-v1.2/tree/v1.2.0 for the released v1.2 of the Common Workflow Language standards and the history of its development.
 
-You can render this using https://github.com/common-workflow-language/cwl-website/blob/master/website.sh
+You can render this using https://github.com/common-workflow-language/cwl-website/blob/main/website.sh
 
 You may browse the released v1.2 standards online at https://www.commonwl.org/v1.2

Workflow.yml

@@ -45,7 +45,7 @@ $graph:
       should be trivially updatable by changing `cwlVersion`, however
       CWL documents that relied on previously undefined or
       underspecified behavior may have slightly different behavior in
-      v1.2.
+      v1.2.  See note about `cwl-upgrader` in the changelog.
 
       ## Changelog
 
@@ -74,7 +74,10 @@ $graph:
 
       See also the [CWL Command Line Tool Description, v1.2 changelog](CommandLineTool.html#Changelog).
       For other changes since CWL v1.0, see the
-      [CWL Workflow Description, v1.1 changelog](https://www.commonwl.org/v1.1/Workflow.html#Changelog)
+      [CWL Workflow Description, v1.1 changelog](https://www.commonwl.org/v1.1/Workflow.html#Changelog).
+
+      [`cwl-upgrader`](https://github.com/common-workflow-language/cwl-upgrader) can
+      be used for upgrading CWL documents from version `draft-3`, `v1.0`, and `v1.1` to `v1.2`.
 
       ## Purpose
 
@@ -616,7 +619,8 @@ $graph:
         _type: "@id"
         subscope: run
       doc: |
-        Specifies the process to run.
+        Specifies the process to run.  If `run` is a string, it must be an absolute IRI
+        or a relative path from the primary document.
     - name: when
       type:
         - "null"

concepts.md

@@ -61,7 +61,7 @@ the CWL specification.
 ## Data concepts
 
 An **object** is a data structure equivalent to the "object" type in JSON,
-consisting of a unordered set of name/value pairs (referred to here as
+consisting of an unordered set of name/value pairs (referred to here as
 **fields**) and where the name is a string and the value is a string, number,
 boolean, array, or object.
 
@@ -100,12 +100,12 @@ must declare the `cwlVersion` of that document.  Implementations must
 validate against the document's declared version.  Implementations
 should allow workflows to reference documents of both newer and older
 CWL versions (up to the highest version of CWL supported by that
-implementation).  Where the runtime enviroment or runtime behavior has
+implementation).  Where the runtime environment or runtime behavior has
 changed between versions, for that portion of the execution an
-implementation must provide runtime enviroment and behavior consistent
+implementation must provide runtime environment and behavior consistent
 with the document's declared version.  An implementation must not
 expose a newer feature when executing a document that specifies an
-older version that does not not include that feature.
+older version that does not include that feature.
 
 ### map
 
@@ -115,7 +115,7 @@ Note: This section is non-normative.
 
 The above syntax in the CWL specifications means there are two or more ways to write the given value.
 
-Option one is a array and is the most verbose option.
+Option one is an array and is the most verbose option.
 
 Option one generic example:
 ```
@@ -191,7 +191,7 @@ hints:
         version: [ "1.0" ]
       python: {}
 ```
-`
+
 Sometimes we have a third and even more compact option denoted like this:
 > type: array<ComplexType> |
 > map<`key_field`, `field2` | ComplexType>
@@ -297,8 +297,8 @@ which the `id` field is explicitly listed in this specification.
 ## Document preprocessing
 
 An implementation must resolve [$import](SchemaSalad.html#Import) and
-[$include](SchemaSalad.html#Import) directives as described in the
-[Schema Salad specification](SchemaSalad.html).
+[$include](SchemaSalad.html#Include) directives as described in the
+[Schema Salad specification](SchemaSalad.html#Document_preprocessing).
 
 Another transformation defined in Schema salad is simplification of data type definitions.
 Type `<T>` ending with `?` should be transformed to `[<T>, "null"]`.
@@ -376,7 +376,7 @@ produces output, and then terminates.
 
 A **workflow** is a process characterized by multiple subprocess steps,
 where step outputs are connected to the inputs of downstream steps to
-form a directed acylic graph, and independent steps may run concurrently.
+form a directed acyclic graph, and independent steps may run concurrently.
 
 A **runtime environment** is the actual hardware and software environment when
 executing a command line tool.  It includes, but is not limited to, the
@@ -421,7 +421,7 @@ of [process requirements](#Requirements_and_hints).
 ## Generic execution process
 
 The generic execution sequence of a CWL process (including workflows
-and command line line tools) is as follows.  Processes are
+and command line tools) is as follows.  Processes are
 modeled as functions that consume an input object and produce an
 output object.