update changelog and tests

galaxyproject · Sep 11, 2023 · 85c0caf · 85c0caf
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diff --git a/workflows/transcriptomics/rnaseq-pe/CHANGELOG.md b/workflows/transcriptomics/rnaseq-pe/CHANGELOG.md
@@ -3,7 +3,12 @@
 ## [0.5] 2023-03-17
 
 ### Automatic update
-- `toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.10b+galaxy2`
+- `toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.10b+galaxy4`
+
+### Manual update
+- Use STAR to compute normalized strand splitted coverage
+- Propose StringTie to compute FPKM etc...
+- Put cufflinks step optional
 
 ## [0.4] 2023-01-16
 

diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml
@@ -24,7 +24,6 @@
     reverse_adapter: GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
     reference_genome: dm6
     strandness: unstranded
-    split coverage by strand: true
     cufflinks_FPKM: false
     stringtie_FPKM: true
   outputs:
@@ -85,6 +84,12 @@
           asserts:
             has_text:
               text: "FBgn0010247\t13"
+    both strands coverage:
+      element_tests:
+        GSM461177:
+            has_size:
+              value: 9885639
+              delta: 900000
     stranded coverage:
       element_tests:
         GSM461177_reverse: