Updated SBG Manifest Cypher query

queries/ctdc_queires.cypher

@@ -13,20 +13,21 @@ RETURN t.clinical_trial_id AS Trial_ID, t.clinical_trial_designation AS Trial_Co
 
 
 // Final version to generate SBG manifest
-MATCH (t:clinical_trial)<--(a:arm)<--(c:case)<--(s:specimen)<--(n:nucleic_acid)<-[*]-(f:file), (s)<-[*]-(ar:assignment_report)
-WITH DISTINCT f, t, a, c, ar, s, n
+MATCH(t:clinical_trial)<--(a:arm)<--(c:case)<--(s:specimen)<--(n:nucleic_acid)<--(sa:sequencing_assay)<--(f:file),
+     (s)<-[*]-(ar:assignment_report), (sa)<--(v:variant_report)
+WITH DISTINCT f, t, a, c, ar, s, n, sa, v
 OPTIONAL MATCH (s)<--(i_pten:ihc_assay_report)
   WHERE i_pten.ihc_test_gene = 'PTEN'
-WITH DISTINCT f, t, a, c, ar, s, n, i_pten
+WITH DISTINCT f, t, a, c, ar, s, n, sa, v, i_pten
 OPTIONAL MATCH (s)<--(i_msh2:ihc_assay_report)
   WHERE i_msh2.ihc_test_gene = 'MSH2'
-WITH DISTINCT f, t, a, c, ar, s, n, i_pten, i_msh2
+WITH DISTINCT f, t, a, c, ar, s, n, sa, v, i_pten, i_msh2
 OPTIONAL MATCH (s)<--(i_mlh1:ihc_assay_report)
   WHERE i_mlh1.ihc_test_gene = 'MLH1'
-WITH DISTINCT f, t, a, c, ar, s, n, i_pten, i_msh2, i_mlh1
+WITH DISTINCT f, t, a, c, ar, s, n, sa, v, i_pten, i_msh2, i_mlh1
 OPTIONAL MATCH (s)<--(i_rb:ihc_assay_report)
   WHERE i_rb.ihc_test_gene = 'RB'
-WITH DISTINCT f, t, a, c, ar, s, n, i_pten, i_msh2, i_mlh1, i_rb
+WITH DISTINCT f, t, a, c, ar, s, n, sa, v, i_pten, i_msh2, i_mlh1, i_rb
 RETURN t.clinical_trial_id AS Trial_ID, t.clinical_trial_designation AS Trial_Code,
        a.arm_id AS Treatment_Arm,
        c.case_id AS Case_ID, c.gender AS Gender, c.race AS Race, c.ethnicity AS Ethnicity, c.disease AS Diagnosis,
@@ -40,8 +41,14 @@ RETURN t.clinical_trial_id AS Trial_ID, t.clinical_trial_designation AS Trial_Co
        coalesce(i_msh2.ihc_test_result, 'UNKNOWN') AS MSH2_IHC_Status,
        coalesce(i_rb.ihc_test_result, 'UNKNOWN') AS RB_IHC_Status,
        ar.assignment_outcome AS Assignment_Outcome,
-       'Targeted NGS' AS `Experimental_strategy`,
-       'Ion Torrent' AS Platform,
-       'GRCh37' AS Reference_genome,
+       sa.experimental_method + ':' + CASE f.file_type
+         WHEN 'Aligned DNA reads file' THEN ' DNA'
+         WHEN 'Aligned RNA reads file' THEN ' RNA'
+         WHEN 'Variants file' THEN ' DNA/RNA'
+         WHEN 'Index file' THEN ' '
+         END AS `Experimental_strategy`,
+       sa.platform AS Platform,
+       v.reference_genome AS Reference_genome,
        f.uuid AS File_UUID, f.file_name AS File_Name, f.file_type AS File_Type, f.file_size AS File_Size,
-       f.md5sum AS md5sum, f.file_location AS File_Location, 'dg.4DFC/' + f.uuid AS GUID
+       f.md5sum AS md5sum, f.file_location AS File_Location, 'dg.4DFC/' + f.uuid AS GUID
+  ORDER BY Case_ID, File_Name