[MNT] Update default Neurobagel SPARQL query file and turn into PR ch…

…eckbox (#359)

* add PR checkbox for regenerating default query file

* regenerate default query file

.github/pull_request_template.md

@@ -34,6 +34,7 @@ _This section is for the PR reviewer_
 - [ ] PR links to GitHub issue with mention `Closes #XXXX`
 - [ ] Tests pass
 - [ ] Checks pass
+- [ ] If the PR changes the SPARQL query template, the default Neurobagel query file has also been [regenerated](https://github.com/neurobagel/api?tab=readme-ov-file#the-default-neurobagel-sparql-query)
 
 For new features:
 - [ ] Tests have been added

docs/default_neurobagel_query.rq

@@ -4,9 +4,11 @@ PREFIX nbg: <http://neurobagel.org/graph/>
 PREFIX ncit: <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#>
 PREFIX nidm: <http://purl.org/nidash/nidm#>
 PREFIX snomed: <http://purl.bioontology.org/ontology/SNOMEDCT/>
+PREFIX np: <https://github.com/nipoppy/pipeline-catalog/tree/main/processing/>
 
 SELECT DISTINCT ?dataset_uuid ?dataset_name ?dataset_portal_uri ?sub_id ?age ?sex
-?diagnosis ?subject_group ?num_matching_phenotypic_sessions ?num_matching_imaging_sessions ?session_id ?session_type ?assessment ?image_modal ?session_file_path ?pipeline_name ?pipeline_version
+?diagnosis ?subject_group ?num_matching_phenotypic_sessions ?num_matching_imaging_sessions
+?session_id ?session_type ?assessment ?image_modal ?session_file_path ?pipeline_name ?pipeline_version
 WHERE {
     ?dataset_uuid a nb:Dataset;
         nb:hasLabel ?dataset_name;
@@ -41,6 +43,7 @@ WHERE {
 
         } GROUP BY ?subject
     }
+
     OPTIONAL {
         ?session nb:hasCompletedPipeline ?pipeline.
         ?pipeline nb:hasPipelineVersion ?pipeline_version.