updating the preprocessing workflow replacing the decompressing step …

…with an update to Krakentool, and also pushing the latest updates to the workflows, still the planemo tests fails for the same reasons, I need help with that
galaxyproject · Jun 28, 2023 · 4461da3 · 4461da3
1 parent 121bac4
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diff --git a/...-nanopore-all-samples-analysis/Pathogen-Detection-Nanopore-All-Samples-Analysis-tests.yml b/...-nanopore-all-samples-analysis/Pathogen-Detection-Nanopore-All-Samples-Analysis-tests.yml
@@ -1,15 +1,5 @@
 - doc: Test outline for Pathogen-Detection-Nanopore-All-Samples-Analysis
   job:
-    Contigs:
-      class: Collection
-      collection_type: list
-      elements:
-      - class: File
-        identifier: Contigs
-        path: test-data/Contigs_Contigs.fasta
-      - class: File
-        identifier: Contigs (1)
-        path: test-data/Contigs_Contigs (1).fasta
     VFs:
       class: Collection
       collection_type: list
@@ -20,6 +10,16 @@
       - class: File
         identifier: VFs (1)
         path: test-data/VFs_VFs (1).tabular
+    Contigs:
+      class: Collection
+      collection_type: list
+      elements:
+      - class: File
+        identifier: Contigs
+        path: test-data/Contigs_Contigs.fasta
+      - class: File
+        identifier: Contigs (1)
+        path: test-data/Contigs_Contigs (1).fasta
     VFs accessions:
       class: Collection
       collection_type: list
@@ -42,7 +42,7 @@
         path: test-data/VFs accessions with SampleID_VFs accessions with SampleID
           (1).tabular
   outputs:
-    'ClustalW on input dataset(s): dnd':
+    Adjusted ABRicate VFs tabular part1:
       element_tests:
-        NP_757239:
-          path: 'test-data/ClustalW on input dataset(s): dnd_NP_757239.nhx'
+        NP_462663:
+          path: test-data/Adjusted ABRicate VFs tabular part1_NP_462663.tabular