run the workflow with a smaller kraken db : viruses

Delphine-L · Dec 12, 2022 · 2c4894a · 2c4894a
1 parent 52dd552
commit 2c4894a
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Showing 2 changed files with 17 additions and 17 deletions.
diff --git a/...-assembly-v2/VGP-Decontamination/VGP-Decontamination-pipeline---Db-not-included-tests.yml b/...-assembly-v2/VGP-Decontamination/VGP-Decontamination-pipeline---Db-not-included-tests.yml
@@ -2,19 +2,19 @@
   job:
     Scaffolded assembly (fasta):
       class: File
-      location: https://www.dropbox.com/s/rl1nkrnicyhgpun/Scaffolded%20assembly%20%28fasta%29.fasta.gz?dl=1
+      path: https://www.dropbox.com/s/rl1nkrnicyhgpun/Scaffolded%20assembly%20%28fasta%29.fasta.gz?dl=1
       filetype: fasta.gz
     Refseq Mitochondrion Database:
       class: File
-      location: https://www.dropbox.com/s/ymm8c4qvxuwwb4u/Refseq%20Mitochondrion%20Database.fasta.gz?dl=1
+      path: https://www.dropbox.com/s/ymm8c4qvxuwwb4u/Refseq%20Mitochondrion%20Database.fasta.gz?dl=1
       filetype: fasta.gz
-    Kraken 2 Database: 2020-11-26T021706Z_standard_kmer-len_35_minimizer-len_31_minimizer-spaces_6_load-factor_0.7
+    Kraken 2 Database: viral2019-03
     Include specific intervals - Optional: null
     SAK input file - Optional: null
   outputs:
-    Decontaminated assembly:
-      checksum: 'sha1$70a3351156b45e1961e7b986f330527a175f9794'
     full contaminant + mito scaffold list:
       file: test-data/full contaminant + mito scaffold list.txt
       compare: diff
       lines_diff: 0
+    Decontaminated assembly:
+     checksum: 'sha1$70a3351156b45e1961e7b986f330527a175f9794'
diff --git a/...ows/VGP-assembly-v2/VGP-Decontamination/VGP-Decontamination-pipeline---Db-not-included.ga b/...ows/VGP-assembly-v2/VGP-Decontamination/VGP-Decontamination-pipeline---Db-not-included.ga
@@ -10,7 +10,7 @@
     ],
     "format-version": "0.1",
     "license": "BSD-3-Clause",
-    "version" : "2.1",
+    "release": "0.1",
     "name": "VGP Decontamination pipeline - Db not included",
     "steps": {
         "0": {
@@ -439,13 +439,13 @@
             "workflow_outputs": [
                 {
                     "label": null,
-                    "output_name": "classified_out_s",
-                    "uuid": "359c8d03-f7b4-469d-a832-65f1001f8d39"
+                    "output_name": "output",
+                    "uuid": "f501149f-fe9f-4e8d-8fbf-c9c33312aa7e"
                 },
                 {
                     "label": null,
-                    "output_name": "output",
-                    "uuid": "f501149f-fe9f-4e8d-8fbf-c9c33312aa7e"
+                    "output_name": "classified_out_s",
+                    "uuid": "359c8d03-f7b4-469d-a832-65f1001f8d39"
                 }
             ]
         },
@@ -615,13 +615,13 @@
             "workflow_outputs": [
                 {
                     "label": null,
-                    "output_name": "mito_scaff_names",
-                    "uuid": "a1c20e74-b2ed-4c86-9495-c11948664a14"
+                    "output_name": "cov_report",
+                    "uuid": "96d9a9d3-04c6-4c12-b996-a7067b931f4f"
                 },
                 {
                     "label": null,
-                    "output_name": "cov_report",
-                    "uuid": "96d9a9d3-04c6-4c12-b996-a7067b931f4f"
+                    "output_name": "mito_scaff_names",
+                    "uuid": "a1c20e74-b2ed-4c86-9495-c11948664a14"
                 }
             ]
         },
@@ -829,7 +829,7 @@
             },
             "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
             "tool_shed_repository": {
-                "changeset_revision": "f46f0e4f75c4",
+                "changeset_revision": "d698c222f354",
                 "name": "text_processing",
                 "owner": "bgruening",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
@@ -905,5 +905,5 @@
     },
     "tags": [],
     "uuid": "b48b47f2-264a-410c-9db6-6e3a1c9a2359",
-    "version": 1
-}
+    "version": 0
+}