Merge pull request galaxyproject#490 from Delphine-L/report8

VGP 8 - addition of workflow report
Delphine-L · Jul 31, 2024 · a919037 · a919037
2 parents 975a339 + 4dc29d3
commit a919037
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diff --git a/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/CHANGELOG.md b/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/CHANGELOG.md
@@ -1,5 +1,9 @@
 # Changelog
 
+## [0.2.5] 2024-07-31
+
+- Addition of Workflow report
+
 ## [0.2.4] 2024-05-20
 
 ### Automatic update

diff --git a/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8.ga b/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8.ga
@@ -15,8 +15,11 @@
     ],
     "format-version": "0.1",
     "license": "CC-BY-4.0",
-    "release": "0.2.4",
+    "release": "0.2.5",
     "name": "Scaffolding-HiC-VGP8",
+    "report": {
+        "markdown": "# Workflow Execution Report\n\nTime workflow was invoked\n\n```galaxy\ninvocation_time()\n```\n\n```galaxy\ngenerate_galaxy_version()\n```\n\n\n## BUSCO results (Vertebrata database)\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Busco Summary image\")\n```\n\n\n## Assembly statistics\n\n\n```galaxy\nhistory_dataset_as_table(output=\"clean_stats\")\n```\n\n\n## Nx and Size plots\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Nx Plot\")\n```\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Size Plot\")\n```\n\n## PretextMap\n\n### Before Scaffolding\n\n\r\n```galaxy\nhistory_dataset_as_image(output=\"Pretext Map Before HiC scaffolding\")\n```\r\n\n\n### After Scaffolding\r\n```galaxy\nhistory_dataset_as_image(output=\"Pretext Map After HiC scaffolding\")\n```\r\n\n\n\n\n## Current Workflow\n```galaxy\nworkflow_display()\n```\n"
+    },
     "steps": {
         "0": {
             "annotation": "The input GFA must conform to gfa1.2 standards, i.e. should have 'P' lines defined. Output GFAs from assemblers can be run through a GFA-&gt;GFA conversion using gfastats to ensure this. \n",
@@ -74,7 +77,7 @@
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@@ -107,7 +110,7 @@
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@@ -194,7 +197,7 @@
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@@ -1146,21 +1149,72 @@
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-                    "label": "Busco Summary",
-                    "output_name": "busco_sum",
-                    "uuid": "49589149-e16f-4a88-9d84-c1b06288021f"
-                },
                 {
                     "label": "Busco Summary image",
                     "output_name": "summary_image",
                     "uuid": "cf7a5b93-9021-4029-8107-015787fa2ca5"
+                },
+                {
+                    "label": "Busco Summary",
+                    "output_name": "busco_sum",
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+                    "output_name": "stats"
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+            "label": null,
+            "name": "Replace",
+            "outputs": [
+                {
+                    "name": "outfile",
+                    "type": "input"
+                }
+            ],
+            "position": {
+                "left": 4038.9643691913197,
+                "top": 1953.52949196313
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+            "post_job_actions": {
+                "HideDatasetActionoutfile": {
+                    "action_arguments": {},
+                    "action_type": "HideDatasetAction",
+                    "output_name": "outfile"
+                }
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+            "tool_shed_repository": {
+                "changeset_revision": "fbf99087e067",
+                "name": "text_processing",
+                "owner": "bgruening",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
+            "tool_state": "{\"find_and_replace\": [{\"__index__\": 0, \"find_pattern\": \"#\", \"replace_pattern\": \"Number of\", \"is_regex\": false, \"global\": true, \"caseinsensitive\": false, \"wholewords\": false, \"skip_first_line\": false, \"searchwhere\": {\"searchwhere_select\": \"line\", \"__current_case__\": 0}}], \"infile\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "9.3+galaxy1",
+            "type": "tool",
+            "uuid": "4b0a88b6-47cc-4381-949c-fc18a99799ac",
+            "when": null,
+            "workflow_outputs": [
+                {
+                    "label": "clean_stats",
+                    "output_name": "outfile",
+                    "uuid": "6013195c-2adc-4f6f-8193-199f97b711c9"
+                }
+            ]
+        },
+        "25": {
+            "annotation": "",
+            "id": 25,
             "input_connections": {
                 "gfa_stats": {
                     "id": 20,
@@ -1520,7 +1574,7 @@
                         ]
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@@ -1529,11 +1583,11 @@
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@@ -1580,14 +1634,14 @@
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@@ -1613,14 +1667,14 @@
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@@ -1804,14 +1858,14 @@
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@@ -1864,14 +1918,14 @@
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@@ -1916,14 +1970,14 @@
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@@ -1963,14 +2017,14 @@
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@@ -2014,6 +2068,6 @@
     "tags": [
         "VGP_curated"
     ],
-    "uuid": "a45c5bd9-6b56-40ff-a9ea-ba420a683f42",
-    "version": 3
-}
+    "uuid": "88cb8c3c-791b-4ab8-b982-4811f6f94630",
+    "version": 5
+}