Updating workflows/VGP-assembly-v2/Assembly-decontamination-VGP9 from 0.3 to 0.4

workflows/VGP-assembly-v2/Assembly-decontamination-VGP9/Assembly-decontamination-VGP9.ga

@@ -11,7 +11,7 @@
     ],
     "format-version": "0.1",
     "license": "BSD-3-Clause",
-    "release": "0.3",
+    "release": "0.4",
     "name": "Assembly-decontamination-VGP9",
     "report": {
         "markdown": "\n# Workflow Execution Report\n\n### Worflow ran on: \n\n```galaxy\ninvocation_time()\n```\n\n# List of contaminants\n\n\r\n```galaxy\nhistory_dataset_as_table(output=\"contaminants_table\")\n```\r\n\n\n# List of Mitochondrial scaffolds\n\r\n```galaxy\nhistory_dataset_as_table(output=\"mito_scaff_names\")\n```\r\n\n\n\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
@@ -64,7 +64,7 @@
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-            "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}",
+            "tool_state": "{\"validators\": [], \"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}",
             "tool_version": null,
             "type": "parameter_input",
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@@ -124,7 +124,7 @@
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@@ -160,15 +160,15 @@
                     "output_name": "output"
                 }
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-            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.5+galaxy0",
             "tool_shed_repository": {
-                "changeset_revision": "86755160afbf",
+                "changeset_revision": "3dc70b59608c",
                 "name": "text_processing",
                 "owner": "bgruening",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
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-            "tool_version": "9.3+galaxy1",
+            "tool_state": "{\"adv_opts\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"code\": \"/^>/!y/atcgn/NNNNN/\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "9.5+galaxy0",
             "type": "tool",
             "uuid": "5089350b-c1a9-498a-9786-9864d484f77a",
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@@ -448,7 +448,7 @@
                 }
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-            "tool_state": "{\"columnList\": \"c2\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_state": "{\"columnList\": \"c2\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
             "tool_version": "1.0.2",
             "type": "tool",
             "uuid": "8cc3e58f-2940-454a-9cf6-b32c1ab19016",
@@ -457,7 +457,7 @@
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+            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.5+galaxy0",
             "errors": null,
             "id": 10,
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@@ -486,15 +486,15 @@
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-            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.5+galaxy0",
             "tool_shed_repository": {
-                "changeset_revision": "86755160afbf",
+                "changeset_revision": "3dc70b59608c",
                 "name": "text_processing",
                 "owner": "bgruening",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
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-            "tool_version": "9.3+galaxy1",
+            "tool_version": "9.5+galaxy0",
             "type": "tool",
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@@ -508,7 +508,7 @@
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@@ -535,15 +535,15 @@
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             "tool_shed_repository": {
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+                "changeset_revision": "50b6ec4074f4",
                 "name": "gfastats",
                 "owner": "bgruening",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
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             "type": "tool",
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@@ -561,4 +561,4 @@
     ],
     "uuid": "aa4960d9-198d-4990-a393-a98efcd3070a",
     "version": 3
-}
+}

workflows/VGP-assembly-v2/Assembly-decontamination-VGP9/CHANGELOG.md

@@ -1,5 +1,12 @@
 # Changelog
 
+## [0.4] 2025-03-17
+
+### Automatic update
+- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.5+galaxy0`
+- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.5+galaxy0`
+- `toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.10+galaxy0`
+
 ## [0.3] - 2024-08-26
 
 - Changed the regex to only change the sequences. The workflow is now more robust to different (non VGP) scaffold names and VGP names with prefixes. 

workflows/VGP-assembly-v2/Assembly-decontamination-VGP9/README.md

@@ -0,0 +1,14 @@
+## Decontamination Workflow
+
+Decontamination (foreign contaminants and mitochondrial sequences) of genome assembly after scaffolding step. Part of the VGP Suite. 
+
+### Inputs
+
+- Genome Assembly [fasta]
+- Database for Kraken2. Database containing the possible contaminants.
+
+### Ouput
+
+- List of contaminant scaffolds
+- List of mitochondrial scaffolds
+- Decontaminated assembly