Name: workflows
Owner: C3BI-pasteur-fr
Description: Community maintained workflows & tools (with examples)
Forked from: common-workflow-language/workflows
Created: 2018-04-06 08:19:53.0
Updated: 2018-05-07 12:59:40.0
Pushed: 2018-05-07 12:59:38.0
Size: 3877
Language: Common Workflow Language
GitHub Committers
User | Most Recent Commit | # Commits |
---|
Other Committers
User | Most Recent Commit | # Commits |
---|
“CWL Tools & Workflows” is a community repository CWL tool and workflow descriptions.
To submit a new workflow or tool description please make a pull request against this repository.
Any contribution submitted for inclusion in this repository shall be under the terms and conditions of the Apache License version 2.0 (see LICENSE.txt).
Please follow these recommendations before pull request:
`STAR.cwl
`) if possible (no
conflicts with existing files) and placed into tools directory`bwa-mem.cwl
or ``
samtools-index.cwl````samtools-docker.yml
`) and $import itIncomplete descriptions are welcome as long as they are usable. Sharing early & often is encouraged.
For your convinience an Apache Jena Fuseki SPARQL server is provided. It automaticaly downloads new CWL tool descriptions converts them into XML/RDF format and makes available at https://sparql-test.commonwl.org or https://sparql-cwl.cloudapp.net/ . Each CWL tool becomes a graph that can be queried. Provided sample queries all the graphs where foaf:name “Dobin” is present.
To run a simple query that searches for all graphs(cwl files) where foaf:name is “Dobin”:
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX doap: <http://usefulinc.com/ns/doap#>
SELECT distinct ?file ?name
WHERE {
graph ?file {
?P foaf:name ?name .
FILTER (regex(?name, "Dobin","i"))
}
}
LIMIT 25
If you use different ontologies like schema and foaf you can join them in one query using union:
PREFIX schema: <http://schema.org/>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX adms: <http://www.w3.org/ns/adms#>
SELECT ?file ?name
WHERE {
graph ?file {
{
?P a foaf:Person;
foaf:name ?name.
?x adms:includedAsset ?SSC .
?SSC !schema:Thing+ ?P .
FILTER (regex(?name, "Dobin","i"))
}
union {
?P a schema:Person;
schema:name ?name.
?SSC a schema:SoftwareSourceCode .
?file ?direct ?SSC .
?SSC !schema:Thing+ ?P .
FILTER (regex(?name, "Karimi","i"))
}
}
}
If you provide DOI url and use it as id for a class, it will be automaticaly pulled into default graph. You can query DOI information to find corresponding CWL:
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX schema: <http://schema.org/>
SELECT distinct ?file ?DOI ?name
WHERE {
?DOI ?direct0 ?P .
?P foaf:name ?name .
FILTER (regex(?name, "Lorincz","i"))
GRAPH ?file {
?SSC a schema:SoftwareSourceCode .
?file ?direct1 ?SSC .
?SSC !schema:Thing+ ?DOI .
}
}
Another one:
PREFIX schema: <http://schema.org/>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
select distinct ?file ?name
where {
?pub !schema:Thing+ ?Person .
?Person foaf:name ?name .
graph ?file {
?SSC schema:publication ?pub .
}
}
Test directory includes:
To test tools run `test/test.sh
` from the repository root.