update workflow and tests

galaxyproject · Sep 5, 2023 · 35e0856 · 35e0856
1 parent 18798b3
commit 35e0856
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diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml
@@ -24,6 +24,9 @@
     reverse_adapter: GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
     reference_genome: dm6
     strandness: unstranded
+    split coverage by strand: true
+    cufflinks_FPKM: false
+    stringtie_FPKM: true
   outputs:
     output_log:
       element_tests:
@@ -82,33 +85,19 @@
           asserts:
             has_text:
               text: "FBgn0010247\t13"
-    transcripts_expression:
+    stranded coverage:
       element_tests:
-        GSM461177:
-          asserts:
-            has_text:
-              text: "FBtr0078104\t-\t-\tFBgn0031217\tCG11377\t-\tchr2L:102379-104142\t1583\t1.95689	28.9556	19.9177	37.9936\tOK"
-    genes_expression:
-      element_tests:
-        GSM461177:
-          asserts:
-            has_text:
-              text: "FBgn0031217\t-\t-\tFBgn0031217\tCG11377\t-\tchr2L:102379-104142\t-\t-\t28.9556	19.7218	38.1895\tOK"
-    both strands coverage:
-      element_tests:
-        GSM461177:
-            has_size:
-              value: 9885639
-              delta: 900000
-    negative strand coverage:
-      element_tests:
-        GSM461177:
+        GSM461177_reverse:
             has_size:
               value: 7756965
               delta: 700000
-    positive strand coverage:
-      element_tests:
-        GSM461177:
+        GSM461177_forward:
             has_size:
               value: 7756965
               delta: 700000
+    genes_expression_stringtie:
+      element_tests:
+        GSM461177:
+          asserts:
+            has_text:
+              text: "FBgn0031217 	CG11377 	chr2L 	+ 	102380 	104142 	1.003790 	31.826454 	55.206604"