fixed missing contaminant bugs and changed tests

Delphine-L · Aug 15, 2024 · 7dc9798 · 7dc9798
1 parent 8b3d69d
commit 7dc9798
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diff --git a/...ows/VGP-assembly-v2/Assembly-decontamination-VGP9/Assembly-decontamination-VGP9-tests.yml b/...ows/VGP-assembly-v2/Assembly-decontamination-VGP9/Assembly-decontamination-VGP9-tests.yml
@@ -2,16 +2,20 @@
   job:
     Scaffolded assembly (fasta):
       class: File
-      location: https://zenodo.org/records/10067431/files/Scaffolded_assembly.fasta?download=1
+      location: https://zenodo.org/records/13326708/files/Scaffolded_assembly.fasta?download=1
       filetype: fasta
-    Database for Kraken2: viral2019-03
+    Database for Kraken2: k2_pluspf_20210517
   outputs:
-    full contaminant + mito scaffold list:
-      file: test-data/full contaminant + mito scaffold list.txt
-      compare: diff
-      sort: true
+    mito_scaff_names:
+      asserts:
+        has_text: 
+          text: "SCAFFOLD_82"
     final decontaminated assembly:
       decompress: true
       asserts:
         not_has_text: 
-          text: "_1100"
+          text: "scaffold_115"
+    contaminants_table:
+      asserts:
+        has_text: 
+          text: "SCAFFOLD_101"