updating the SNP workflow to solve the testing issue

galaxyproject · Aug 4, 2023 · b3575ec · b3575ec
1 parent 486c419
commit b3575ec
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Showing 4 changed files with 9,554 additions and 82,534 deletions.
diff --git a/...dentification/Pathogen-Detection-Nanopore-SNP-based-pathogenetic-Identification-tests.yml b/...dentification/Pathogen-Detection-Nanopore-SNP-based-pathogenetic-Identification-tests.yml
@@ -15,7 +15,7 @@
         identifier: Spike3bBarcode10
         path: test-data/nanopore_preprocessed_reads_collection_Spike3bBarcode10.fastq.gz
   outputs:
-    bcftools_consensus:
+    extracted_fields_from_the_vcf_output:
       element_tests:
         Spike3bBarcode10:
-          path: test-data/bcftools_consensus_Spike3bBarcode10.fasta
+          path: test-data/extracted_fields_from_the_vcf_output_Spike3bBarcode10.tabular
diff --git a/...netic-identification/Pathogen-Detection-Nanopore-SNP-based-pathogenetic-Identification.ga b/...netic-identification/Pathogen-Detection-Nanopore-SNP-based-pathogenetic-Identification.ga
@@ -105,6 +105,13 @@
                     },
                     "action_type": "ChangeDatatypeAction",
                     "output_name": "output1"
+                },
+                "RenameDatasetActionoutput1": {
+                    "action_arguments": {
+                        "newname": "decompressed_rg_file"
+                    },
+                    "action_type": "RenameDatasetAction",
+                    "output_name": "output1"
                 }
             },
             "tool_id": "CONVERTER_gz_to_uncompressed",
@@ -250,6 +257,11 @@
             "uuid": "a98868a2-3706-4ba3-8650-e5b692be654e",
             "when": null,
             "workflow_outputs": [
+                {
+                    "label": "clair3_full_alignment_vcf",
+                    "output_name": "full_alignment",
+                    "uuid": "049c1a4a-5376-4d8d-a798-08fed282e912"
+                },
                 {
                     "label": "clair3_merged_output",
                     "output_name": "merge_output",
@@ -259,11 +271,6 @@
                     "label": "clair3_pileup_vcf",
                     "output_name": "pileup",
                     "uuid": "2b223463-4015-4a32-a339-85f24debed76"
-                },
-                {
-                    "label": "clair3_full_alignment_vcf",
-                    "output_name": "full_alignment",
-                    "uuid": "049c1a4a-5376-4d8d-a798-08fed282e912"
                 }
             ]
         },
@@ -499,6 +506,6 @@
         "IWC",
         "name:Collection"
     ],
-    "uuid": "44349af3-2187-4b7b-891f-ffab096219c2",
-    "version": 2
+    "uuid": "2aee91bb-8f4d-4c16-81b2-95a57cc08028",
+    "version": 4
 }