This might actually generate soft file with raw & supplemental data.

[htsworkflow.git] / htsworkflow / templates / geo_files.sparql

diff --git a/htsworkflow/templates/geo_files.sparql b/htsworkflow/templates/geo_files.sparql
index 7b66f4f174f15d78b4b26bd2985522d37bc35827..6fd7cac6ad92a92517b38240c0cf1b7ccbc57d70 100644 (file)
--- a/htsworkflow/templates/geo_files.sparql
+++ b/htsworkflow/templates/geo_files.sparql
@@ -3,10 +3,12 @@ PREFIX submissionOntology: <http://jumpgate.caltech.edu/wiki/UcscSubmissionOntol
 PREFIX ucscDaf: <http://jumpgate.caltech.edu/wiki/UcscDaf#>
 PREFIX ncbiTaxon: <http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=>
 PREFIX geoSoft: <http://www.ncbi.nlm.nih.gov/geo/info/soft2.html#>
+PREFIX dc: <http://purl.org/dc/elements/1.1/>
 
-select distinct ?filename, ?md5sum, ?file_type ?file_type_label
+select distinct ?filename, ?md5sum, ?file_type ?file_type_label ?flowcell_id ?read_length ?flowcell_type ?image_software ?image_version ?basecall_software ?basecall_version ?sequencer_model
 WHERE {
   <{{submission}}> ucscDaf:has_file ?file ;
+                   submissionOntology:library ?library ;
                    a submissionOntology:submission .
 
   ?file ucscDaf:filename ?filename ;
@@ -15,4 +17,16 @@ WHERE {
   ?file_type a <{{file_class}}> ;
              geoSoft:fileTypeLabel ?file_type_label .
 
+  OPTIONAL { ?file dc:source ?source_file .
+             ?source_file libraryOntology:flowcell ?flowcell .
+             ?flowcell libraryOntology:flowcell_id ?flowcell_id ;
+                       libraryOntology:read_length ?read_length ;
+                       libraryOntology:flowcell_type ?flowcell_type ;
+                       libraryOntology:image_software ?image_software ;
+                       libraryOntology:image_version ?image_version ;
+                       libraryOntology:basecall_software ?basecall_software ;
+                       libraryOntology:basecall_version ?basecall_version ;
+                       libraryOntology:sequenced_by ?sequencer .
+             ?sequencer libraryOntology:sequencer_model ?sequencer_model
+  }
 }
\ No newline at end of file