Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add doc for SecondaryFileSchema, plus minor fixes #70

Open
wants to merge 4 commits into
base: master
Choose a base branch
from
Open

Add doc for SecondaryFileSchema, plus minor fixes #70

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
d6c6265
Fix secondaryFiles DSL example title
Jan 13, 2020
944d5aa
Add doc for SecondaryFileSchema
Jan 13, 2020
c157f7e
Fix broken links
Jan 13, 2020
e21b6a0
Update doc for SecondaryFileSchema
Jan 13, 2020
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
14 changes: 14 additions & 0 deletions Process.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -939,6 +939,20 @@ $graph:
set to `false` and the expected secondary file does not exist.
Default value for `required` field is `true` for secondary files on
input and `false` for secondary files on output.
doc: |
Secondary files are specified using the following micro-DSL for secondary files:

* If the value is a string, it is transformed to an object with two fields
`pattern` and `required`
* By default, the value of `required` is `null`
(this indicates default behavior, which may be based on the context)
* If the value ends with a question mark `?` the question mark is
stripped off and the value of the field `required` is set to `False`
* The remaining value is assigned to the field `pattern`

For implementation details and examples, please see
[this section](SchemaSalad.html#Domain_Specific_Language_for_secondary_files)
in the Schema Salad specification.

- name: LoadListingRequirement
type: record
Expand Down
4 changes: 2 additions & 2 deletions Workflow.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -103,8 +103,8 @@ $graph:
contain either a non-string value accepted by the field
type, or a valid expression which returns a value having one
of the the other types defined for that field.
* [WorkflowStepInput](WorkflowStepInput) now has a `loadContents` field.
* [WorkflowStepInput.id](WorkflowStepInput) field value does not have to match an
* [WorkflowStepInput](#WorkflowStepInput) now has a `loadContents` field.
* [WorkflowStepInput.id](#WorkflowStepInput) field value does not have to match an
`input.id` value from the process specified in the `run` field.

See also the [CWL Command Line Tool Description, v1.1 changelog](CommandLineTool.html#Changelog).
Expand Down
2 changes: 1 addition & 1 deletion salad/schema_salad/metaschema/sfdsl_res.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@
stripped off and the value of the field `required` is set to `False`
* The remaining value is assigned to the field `pattern`

### Type DSL example
### Secondary files DSL example

Given the following schema:

Expand Down