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v1.0/CommandLineTool.yml

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@@ -225,7 +225,7 @@ $graph:
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doc: |
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Evaluate an expression to generate the output value. If `glob` was
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specified, the value of `self` must be an array containing file objects
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that were matched. If no files were matched, `self' must be a zero
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that were matched. If no files were matched, `self` must be a zero
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length array; if a single file was matched, the value of `self` is an
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array of a single element. Additionally, if `loadContents` is `true`,
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the File objects must include up to the first 64 KiB of file contents

v1.0/Process.yml

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@@ -21,7 +21,7 @@ $graph:
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- "#Process"
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- type: enum
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name: CWLVersions
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name: CWLVersion
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doc: "Version symbols for published CWL document versions."
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symbols:
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- cwl:draft-2
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unsupported protocol, access denied, or other issue) it must signal an
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error.
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If the `location' field is not provided, the `listing` field must be
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If the `location` field is not provided, the `listing` field must be
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provided. The implementation must assign a unique identifier for
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the `location` field.
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jsonldPredicate: "rdfs:comment"
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doc: "A long, human-readable description of this process object."
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- name: cwlVersion
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type: CWLVersions?
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type: CWLVersion?
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doc: |
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CWL document version. Always required at the document root. Not
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required for a Process embedded inside another Process.

v1.0/Workflow.yml

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- |
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## Introduction to draft 4
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## Introduction to v1.0
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This specification represents the fourth milestone of the CWL group.
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This specification represents the first full release from the CWL group.
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Since draft-3, this draft introduces the following changes and additions:
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* The 'inputs' and 'outputs' fields have been renamed 'in' and 'out'.
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[ScatterFeatureRequirement](#ScatterFeatureRequirement) and
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[SubworkflowFeatureRequirement](#SubworkflowFeatureRequirement) are
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available as standard extensions to core workflow semantics.
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available as standard [extensions](#Extensions_and_Metadata) to core
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workflow semantics.
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fields:
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- name: "class"

v1.0/concepts.md

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@@ -205,7 +205,7 @@ requirements, or a requirement is listed which is not recognized by the
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implementation, it is a fatal error and the implementation must not attempt
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to run the process, unless overridden at user option.
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A **hint** is similar to a requirement, however it is not an error if an
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A **hint** is similar to a requirement; however, it is not an error if an
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implementation cannot satisfy all hints. The implementation may report a
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warning if a hint cannot be satisfied.
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Conforming implementations must support parameter references. Parameter
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references use the following subset of
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[Javascript/ECMAScript 5.1](http://www.ecma-international.org/ecma-262/5.1/)
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syntax but they are designed to not require a Javascript engine for evaluation.
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syntax, but they are designed to not require a Javascript engine for evaluation.
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In the following BNF grammar, character classes and grammar rules are denoted
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In the following BNF grammar, character classes, and grammar rules are denoted
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in '{}', '-' denotes exclusion from a character class, '(())' denotes grouping,
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'|' denotes alternates, trailing '*' denotes zero or more repeats, '+' denote
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one or more repeats, all other characters are literal values.
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one or more repeats, '/' escapes these special characters, and all other
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characters are literal values.
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<p>
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<table class="table">
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Use the following algorithm to resolve a parameter reference:
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1. Match the leading symbol as key
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1. Match the leading symbol as the key
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2. Look up the key in the parameter context (described below) to get the current value.
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It is an error if the key is not found in the parameter context.
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3. If there are no subsequent segments, terminate and return current value
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4. Else, match the next segment
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5. Extract the symbol, string, or index from the segment as key
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5. Extract the symbol, string, or index from the segment as the key
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6. Look up the key in current value and assign as new current value. If
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the key is a symbol or string, the current value must be an object.
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If the key is an index, the current value must be an array or string.
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code fragment wrapped in the `${...}` syntax must be evaluated as a
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[EMACScript function body](http://www.ecma-international.org/ecma-262/5.1/#sec-13)
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for an anonymous, zero-argument function. Expressions must return a valid JSON
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data type: one of null, string, number, boolean, array, object.
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Implementations must permit any syntactically valid Javascript and account
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for nesting of parenthesis or braces and that strings that may contain
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parenthesis or braces when scanning for expressions.
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data type: one of null, string, number, boolean, array, object. Other return
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values must result in a `permanentFailure`. Implementations must permit any
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syntactically valid Javascript and account for nesting of parenthesis or braces
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and that strings that may contain parenthesis or braces when scanning for
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expressions.
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The runtime must include any code defined in the ["expressionLib" field of
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InlineJavascriptRequirement](#InlineJavascriptRequirement) prior to
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Exceptions thrown from an exception must result in a `permanentFailure` of the
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process.
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## Success and failure
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A completed process must result in one of `success`, `temporaryFailure` or
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`permanentFailure` states. An implementation may choose to retry a process
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execution which resulted in `temporaryFailure`. An implementation may
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choose to either continue running other steps of a workflow, or terminate
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immediately upon `permanentFailure`.
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* If any step of a workflow execution results in `permanentFailure`, then the
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workflow status is `permanentFailure`.
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* If one or more steps result in `temporaryFailure` and all other steps
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complete `success` or are not executed, then the workflow status is
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`temporaryFailure`.
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* If all workflow steps are executed and complete with `success`, then the workflow
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status is `success`.
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## Executing CWL documents as scripts
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By convention, a CWL document may begin with `#!/usr/bin/env cwl-runner`

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