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‎CommandLineTool.yml

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## Introduction to the CWL Command Line Tool draft standard v1.2.1
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This specification represents the latest development draft from the
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CWL project. There are no new features nor behavior changes in CWL v1.2.1
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as compared to CWL v1.2. v1.2.1 fixes only typos, adds clarifications,
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and adds additional conformance tests. Some changes to the schema defining
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CWL have been changed to aid the auto-generation of libraries for the reading
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and writing of CWL documents.
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Do not write `cwlVersion: v1.2.1`, that is not a valid version of the CWL
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syntax.
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See also the [Schema-Salad v1.2.1 changelog](SchemaSalad.html#Changelog_for_v1.2.1)
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## Changelog for v1.2.1
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* The schema for `Requirement`s has changed to enable faster parsing by
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autogenerated libraries. The `class` field is now a static enum with a
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single permissible value instead of a generic string (for example:
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`class: DockerRequirement` for a `DockerRequirement` hint or requirement.)
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This allows for autogenerated CWL parsers to recognize any requirement
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immediatelly instead of having to check for matching field names and
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valid values, as was done previously.
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* Likewise, the schema for `CommandLineTool` has changed to enable faster parsing by
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autogenerated libraries. The `class` field is now a static enum with a
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single permissible value (`class: CommandLineTool`) instead of a generic
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string.
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This allows for autogenerated CWL parsers to recognize any `CommandLineTool`
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immediatelly instead of having to check for matching field names and
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valid values, as was done previously.
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* The schema for the `CommandLineBinding.position` field now has an explicit
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default value of `0`. Previously this was only expression textually in
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the description of that field.
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* The schema for the `File.streamable` field now has an explicit default
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value of `false` to match the textual description.
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Note: Other fields like `ResourceRequirement.coresMin`, `.coresMax`,
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`.ramMin`, `.ramMax`, `.tmpdirMin`, `.tmpdirMax` have not had defaults
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set in the schema so that parsers can discriminate easily between a
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value not provided and the default value (`0`).
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* Everywhere the schema allows a value of type `long` we also explictly
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allow a value of type `int`. By JSON rules this is implicit, but by
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making it explicit we aid autogenerated CWL libraries especially in
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languages such as Java.
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* The [difference between `$()` and `${}`](#Expressions_(Optional)) were
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clarified. We now make more explicit that `${...}` evaluates to
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`(function() { ... })()`.
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* The publisher of this document is now explictly named; it is the
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[Common Workflow Language project](https://www.commonwl.org), a member
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project of [Software Freedom Conservancy](https://sfconservancy.org/).
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* The [Parameter References](#Parameter_references) section has been updated
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to clarify ambiguity on `null` and array `.length`. Three conformance tests to
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verify this were added as well (`params_broken_null`, `length_for_non_array`,
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`user_defined_length_in_parameter_reference`).
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* It is now explicit in the description of the `size` field of a
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[`File`](#File) object that `size` is measured in bytes, as was already
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stated in the introduction to the `File` object description.
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* The concept of "opaque identifier(s)"/"opaque strings" as mentioned in the
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[`SecondaryFileSchema`](#SecondaryFileSchema), [Parameter References](#Parameter_references),
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and [Runtime Environment](#Runtime_environment) sections is now defined
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in the newly added [glossary](#Glossary): they are nonsensical values
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that are swapped out with a real value later in the evaluation process.
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Workflow and tool expressions **should not** rely on it nor try to parse it.
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### Updated Conformance Tests for v1.2.1
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* Conformance tests are now refered to by their textual identifiers (`id`). Previously
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this was the `label` field. Tests without a `label`/`id` have been give
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one.
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* `tests/loadContents/cwloutput-nolimit.cwl`: Made explicit that
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`bigstring` is an additional output as generated by the existing
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`mkfilelist.py` script's use of [`cwl.output.json`](#Output_binding).
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* The number of different software containers used in the conformance tests
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has been reduced to four. See [the list in the CONFORMANCE_TESTS.md instructions](https://github.com/common-workflow-language/cwl-v1.2/blob/1.2.1_proposed/CONFORMANCE_TESTS.md#writing-a-new-conformance-test).
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* `tests/secondaryfiles/rename-inputs.cwl` has been simplified by changing
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it to reference another input parameter instead of using `self`. The
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behavior of processing secondary files patterns in order and being able
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to reference earlier ones later is not part of CWL v1.2.
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This doesn't exactly replicate the previous behavior, because it introduces
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a new input parameter, however it does demonstrate the ability to rename
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a file and have it staged as a secondary file without having to use
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`InitialWorkDirRequirement`.
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* `tests/conditionals/cond-wf-002.cwl`, `tests/conditionals/cond-wf-002_nojs.cwl`,
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`tests/conditionals/cond-wf-002_nojs.cwl`, `tests/conditionals/cond-wf-011_nojs.cwl`:
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Marked the outputs as optional to remove ambiguity for these conditional
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`when` tests; allowing conformant CWL runners to be more strict in their
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interpretation of the typing rules, if they choose so.
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* `directory_input_docker` was incorrectly marked as required, it is optional
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unless the feature `ShellCommandRequirement` is stated as being supported.
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* `glob_outside_outputs_fails` was incorrectly marked as required, it is
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optional unlewss the feature `DockerRequirement` is stated as being supported.
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* `stage_file_array` was incorrectly marked as required, it is optional
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unless both the features `InlineJavascriptRequirement` and `DockerRequirement`
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are stated as being supported.
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* `stage_file_array_basename` and `stage_file_array_entryname_overrides` were
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both incorrectly marked as required, they are optional unless the feature
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`InitialWorkDirRequirement` and `InlineJavascriptRequirement` are both
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stated as being supported.
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* `optional_numerical_output_returns_0_not_null` was incorrectly marked as
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required, it is optional unless `InlineJavascriptRequirement` is stated
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as being supported.
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* Made it explicit that if a `CommandLineTool` contains logically chained
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commands (e.g. `echo a && echo b`) then the `stdout` File/object must
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include the output of every command. The `stdout_chained_commands` mandatory
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conformance test was added to verify this.
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* `metadata`: The description and content of this test has been updated to
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be more focused on the metadata present in the CWL file.
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### New Mandatory Conformance Tests for v1.2.1
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* `params_broken_null`: Test parameter reference that refers to
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`null.something`.
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* `length_for_non_array`: Test parameter reference that refers to length
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of non-array input.
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* `user_defined_length_in_parameter_reference`: Test 'length' in a parameter
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reference where it does not refer to length of an array input.
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* `directory_literal_with_literal_file_in_subdir_nostdin`: Test non-`stdin`
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reference to literal `File` via a nested `Directory` literal.
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* `colon_in_paths`: Confirm that colons are tolerated in input paths,
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string values, stdout shortcut, and output file & directory names.
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* `colon_in_output_path`: Confirm that colons are tolerated in output
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directory names.
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* `record_with_default`: Confirm that records with defaults are accepted.
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* `record_outputeval_nojs`: Use of `outputEval` on a record itself, not
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the fields of the record (without javascript). An equivalent test with
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`InlineJavascriptRequirement` was added as well: `record_outputeval`.
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* `runtime-outdir`: Test use of `$(runtime.outdir)` for `outputBinding.glob`.
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* `stdout_chained_commands`: Test that chaining two `echo` calls causes
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the workflow runner to emit the combined output to `stdout`. This is to
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confirm that the workflow runner will **not** create an expression such as
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`echo a && echo b > out.txt`, but instead will produce the correct
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`echo a && echo b`, and capture the output correctly.
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* `record_order_with_input_bindings`: Test sorting arguments at each level
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(`inputBinding` for all levels).
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### New Optional Conformance Tests for v1.2.1
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#### `InlineJavaScriptRequirement`
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* `record_outputeval`: Use of `outputEval` on a record itself, not
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the fields of the record.
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* `staging-basename`: Use of an `ExpressionTool` to change `basename` of
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file, then correctly staging the file using the new name.
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* `js-input-record`: A test case for JavaScript with an input record.
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#### `MultipleInputFeatureRequirement`
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* `multiple-input-feature-requirement`: MultipleInputFeatureRequirement on
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workflow outputs.
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## Introduction to the CWL Command Line Tool standard v1.2
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This specification represents the latest development release from the
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CWL group. Since the v1.1 release, v1.2 introduces the
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Since the v1.1 release, v1.2 introduces the
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following updates to the CWL Command Line Tool standard.
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Documents should use `cwlVersion: v1.2` to make use of new
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syntax and features introduced in v1.2. Existing v1.1 documents

‎Workflow.yml

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## Introduction to the CWL Workflow draft standard v1.2.1
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This specification represents the latest development draft from the
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CWL project. There are no new features nor behavior changes in CWL v1.2.1
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as compared to CWL v1.2. v1.2.1 fixes only typos, adds clarifications,
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and adds additional conformance tests. Some changes to the schema defining
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CWL have been changed to aid the auto-generation of libraries for the reading
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and writing of CWL documents.
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Do not write `cwlVersion: v1.2.1`, that is not a valid version of the CWL
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syntax.
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See also the [CommandLineTool v1.2.1 changelog](CommandLineTool.html#Changelog_for_v1.2.1)
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and the [Schema-Salad v1.2.1 changelog](SchemaSalad.html#Changelog_for_v1.2.1).
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## Changelog for v1.2.1
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* The `Workflow.run` field description now explicitly states that it can
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be either a string referencing an external document or an embedded Process.
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This was previously only stated indirectly.
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* The `outputSource` field of [`WorkflowOutputParameter`](#WorkflowOutputParameter)
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now explictly states that workflow inputs can be referenced. The
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mandatory conformance test `output_reference_workflow_input` has been
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added to confirm this.
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### New Mandatory Conformance tests for v1.2.1
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* `output_reference_workflow_input`: Test direct use of `Workflow` level
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input fields in the outputs.
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### New Optional Conformance Tests for v1.2.1
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#### SchemaDefRequirement
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* `schemadef_types_with_import`: Test `SchemaDefRequirement` with a
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workflow, with the `$import` under types. It is similar to `schemadef-wf`,
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but the `$import` is different.
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#### ScatterFeatureRequirement
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* `simple_simple_scatter`: Two level nested scatter.
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* `dotproduct_simple_scatter`: Two level nested scatter: external
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dotproduct and internal simple.
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* `simple_dotproduct_scatter`: Two level nested scatter: external simple
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and internal dotproduct.
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* `dotproduct_dotproduct_scatter`: Two level nested scatter: external
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dotproduct and internal dotproduct.
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* `flat_crossproduct_simple_scatter`: Two level nested scatter: external
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flat_crossproduct and internal simple.
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* `simple_flat_crossproduct_scatter`: Two level nested scatter: external
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simple and internal flat_crossproduct.
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* `flat_crossproduct_flat_crossproduct_scatter`: Two level nested scatter:
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external flat_crossproduct and internal flat_crossproduct.
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* `nested_crossproduct_simple_scatter`: Two level nested scatter: external
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nested_crossproduct and internal simple.
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* `simple_nested_crossproduct_scatter`: Two level nested scatter: external
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simple and internal nested_crossproduct.
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* `nested_crossproduct_nested_crossproduct_scatter`: Two level nested scatter:
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external nested_crossproduct and internal nested_crossproduct.
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## Introduction to CWL Workflow standard v1.2
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‎salad/schema_salad/metaschema/import_include.md

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It is a fatal error if an import directive refers to an external resource
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or resource fragment which does not exist or is not accessible.
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<a name="import_example" />
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### Import example: replacing the `$import` node
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import.json:

‎salad/schema_salad/metaschema/salad.md

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inherited records can narrow the types of fields if those fields are re-specified
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with a matching jsonldPredicate.
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### Changelog for v1.2.1
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There are no new features nor behavior changes in Schema Salad v1.2.1
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as compared to Schema-Salad v1.2. Schema Sald v1.2.1 only fixes typos and adds
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clarifications.
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* The `salad` directory's contents have been trimmed to the bare necessities.
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The `salad/README.rst` has been refreshed from the [upstream repository](https://github.com/common-workflow-language/schema_salad/).
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* The [existing behviour of `$import`](#Import) has been clarified.
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If the `$import` node is in an array and the import operation yields an
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array, it is flattened to the parent array. Otherwise the `$import`
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node is replaced in the document structure by the object or array yielded
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from the import operation. An [example](#import_example)
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has been added to illustrate this better.
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* A pair of missing brackets was added to the [Type DSL Example](#Type_DSL_example)'s
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example input.
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## References to Other Specifications
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**Javascript Object Notation (JSON)**: http://json.org

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