report if a flowcell was single or paired ended as a file property

diff --git a/htsworkflow/submission/aws_submission.py b/htsworkflow/submission/aws_submission.py
index 17abcbbcfc36344e98701d0ce8fa205c2ca85005..23ba81ac023b86d420ba0cea5e91a1e5e867864f 100644 (file)
--- a/htsworkflow/submission/aws_submission.py
+++ b/htsworkflow/submission/aws_submission.py
@@ -136,6 +136,10 @@ class AWSSubmission(Submission):
         platform_alias = {
             'Illumina HiSeq 2500': 'ENCODE:HiSeq2500'
         }
+        run_type_alias = {
+            'Single': 'single-ended',
+            'Paired': 'paired-ended',
+        }
         query_template = loader.get_template('aws_metadata.sparql')
 
         context = Context({
@@ -152,6 +156,8 @@ class AWSSubmission(Submission):
                 row['platform'] = platform_alias[row['platform']]
             if 'read_length' in row:
                 row['read_length'] = int(row['read_length'])
+            if 'run_type' in row:
+                row['run_type'] = run_type_alias[str(row['run_type'])]
             flowcell_details = {}
             for term in ['machine', 'flowcell', 'lane', 'barcode']:
                 if term in row:

diff --git a/htsworkflow/templates/aws_metadata.sparql b/htsworkflow/templates/aws_metadata.sparql
index dc2ae329c227ff0f82dfb8062c1f2f213fe7c066..0468a231ac5091f1f4868ddf419de4430f57bbe0 100644 (file)
--- a/htsworkflow/templates/aws_metadata.sparql
+++ b/htsworkflow/templates/aws_metadata.sparql
@@ -27,7 +27,8 @@ WHERE {
         a ?fileClass .
 
   ?flowcell_url htswlib:sequenced_by ?machine ;
-            htswlib:flowcell_id ?flowcell .
+            htswlib:flowcell_id ?flowcell ;
+            htswlib:flowcell_type ?run_type .
   ?library htswlib:multiplex_index ?barcode .
 
   ?machine htswlib:sequencer_model ?platform .