Use asserts statements instead of file comparisons

galaxyproject · Feb 14, 2024 · 0fa84dc · 0fa84dc
1 parent 6b2e00c
commit 0fa84dc
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Showing 8 changed files with 31 additions and 1,477 deletions.
diff --git a/workflows/genome-assembly/assembly-with-flye/Genome-assembly-with-Flye-tests.yml b/workflows/genome-assembly/assembly-with-flye/Genome-assembly-with-Flye-tests.yml
@@ -6,31 +6,43 @@
       filetype: fastqsanger.gz
   outputs:
     Flye assembly (consensus):
-      path: test-data/Flye_assembly_consensus.fasta
-      compare: sim_size
-      delta_frac: 0.2
+      asserts:
+        has_text:
+          text: '>contig_1'
+        has_size:
+          min: 80k
+          min: 86k
     Flye assembly (assembly_graph):
-      path: test-data/Flye_assembly.graph_dot
-      compare: sim_size
-      delta_frac: 0.2    
+      asserts:
+        has_text:
+          text: 'digraph {'
+        has_n_lines:
+          min: 20
+          max: 24
     Flye assembly (Graphical Fragment Assembly):
-      path: test-data/Flye_assembly_GFA.txt
-      compare: sim_size
-      delta_frac: 0.2    
+      asserts:
+        has_text:
+          text: edge_1
+        has_n_lines:
+          min: 6
+          max: 8
     Flye assembly (assembly_info):
-      path: test-data/Flye_assembly_info.tabular
-      compare: sim_size
-      delta_frac: 0.2    
+      asserts:
+        - has_text:
+            text: seq_name
+        - has_text:
+            text: contig_1
     'Quast: HTML report':
-      path: test-data/Quast_report.html    
-      compare: sim_size
-      delta_frac: 0.2
+      asserts:
+        has_size:
+          min: 300k
+          max: 400k
     Flye assembly statistics:
-      path: test-data/Flye_assembly_stats.tabular
       asserts: 
         has_text:
           text: "Scaffold L50"
     'Bandage Image: Assembly Graph Image':
-      path: test-data/Bandage_image.jpg
-      compare: sim_size
-      delta_frac: 0.2
+      asserts:
+        has_size:
+          min: 30k
+          max: 50k
diff --git a/workflows/genome-assembly/assembly-with-flye/test-data/Bandage_image.jpg b/workflows/genome-assembly/assembly-with-flye/test-data/Bandage_image.jpg
diff --git a/workflows/genome-assembly/assembly-with-flye/test-data/Flye_assembly.graph_dot b/workflows/genome-assembly/assembly-with-flye/test-data/Flye_assembly.graph_dot
diff --git a/workflows/genome-assembly/assembly-with-flye/test-data/Flye_assembly_GFA.txt b/workflows/genome-assembly/assembly-with-flye/test-data/Flye_assembly_GFA.txt
diff --git a/workflows/genome-assembly/assembly-with-flye/test-data/Flye_assembly_consensus.fasta b/workflows/genome-assembly/assembly-with-flye/test-data/Flye_assembly_consensus.fasta
diff --git a/workflows/genome-assembly/assembly-with-flye/test-data/Flye_assembly_info.tabular b/workflows/genome-assembly/assembly-with-flye/test-data/Flye_assembly_info.tabular
diff --git a/workflows/genome-assembly/assembly-with-flye/test-data/Flye_assembly_stats.tabular b/workflows/genome-assembly/assembly-with-flye/test-data/Flye_assembly_stats.tabular
diff --git a/workflows/genome-assembly/assembly-with-flye/test-data/Quast_report.html b/workflows/genome-assembly/assembly-with-flye/test-data/Quast_report.html