add Busco gff output

Delphine-L · Mar 27, 2024 · c2a75dd · c2a75dd
1 parent 0094cc4
commit c2a75dd
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diff --git a/workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/CHANGELOG.md b/workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/CHANGELOG.md
@@ -1,5 +1,9 @@
 # Changelog
 
+## [0.3.7] 2024-03-27
+
+- Add Gff output to Busco
+
 ## [0.3.6] 2024-03-25
 
 ### Automatic update

diff --git a/workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/Purge-duplicate-contigs-VGP6.ga b/workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/Purge-duplicate-contigs-VGP6.ga
@@ -15,7 +15,7 @@
     ],
     "format-version": "0.1",
     "license": "CC-BY-4.0",
-    "release": "0.3.6",
+    "release": "0.3.7",
     "name": "Purge-duplicate-contigs-VGP6",
     "steps": {
         "0": {
@@ -1082,6 +1082,10 @@
                 }
             },
             "inputs": [
+                {
+                    "description": "runtime parameter for tool Busco",
+                    "name": "input"
+                },
                 {
                     "description": "runtime parameter for tool Busco",
                     "name": "lineage"
@@ -1105,13 +1109,24 @@
                 {
                     "name": "summary_image",
                     "type": "png"
+                },
+                {
+                    "name": "busco_gff",
+                    "type": "gff3"
                 }
             ],
             "position": {
                 "left": 3285.7071094555,
                 "top": 1520.5883525119295
             },
             "post_job_actions": {
+                "TagDatasetActionbusco_gff": {
+                    "action_arguments": {
+                        "tags": "name:p1,busco_p1_gff"
+                    },
+                    "action_type": "TagDatasetAction",
+                    "output_name": "busco_gff"
+                },
                 "TagDatasetActionbusco_missing": {
                     "action_arguments": {
                         "tags": "busco_p1_missing, #p1"
@@ -1148,12 +1163,17 @@
                 "owner": "iuc",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
-            "tool_state": "{\"adv\": {\"evalue\": \"0.001\", \"limit\": \"3\", \"contig_break\": \"10\"}, \"busco_mode\": {\"mode\": \"geno\", \"__current_case__\": 0, \"miniprot\": false, \"use_augustus\": {\"use_augustus_selector\": \"no\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage\": {\"lineage_mode\": \"select_lineage\", \"__current_case__\": 1, \"lineage_dataset\": {\"__class__\": \"ConnectedValue\"}}, \"lineage_conditional\": {\"selector\": \"download\", \"__current_case__\": 1}, \"outputs\": [\"short_summary\", \"missing\", \"image\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_state": "{\"adv\": {\"evalue\": \"0.001\", \"limit\": \"3\", \"contig_break\": \"10\"}, \"busco_mode\": {\"mode\": \"geno\", \"__current_case__\": 0, \"miniprot\": false, \"use_augustus\": {\"use_augustus_selector\": \"no\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"lineage\": {\"lineage_mode\": \"select_lineage\", \"__current_case__\": 1, \"lineage_dataset\": {\"__class__\": \"ConnectedValue\"}}, \"lineage_conditional\": {\"selector\": \"download\", \"__current_case__\": 1}, \"outputs\": [\"short_summary\", \"missing\", \"image\", \"gff\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
             "tool_version": "5.5.0+galaxy0",
             "type": "tool",
             "uuid": "88073363-2f5c-4486-a23a-1cfdc4f5e6a6",
             "when": null,
             "workflow_outputs": [
+                {
+                    "label": "Busco Gff Purged Primary Assembly",
+                    "output_name": "busco_gff",
+                    "uuid": "82fb18a1-ff3a-401c-8c85-910ed255168d"
+                },
                 {
                     "label": "Busco on Purged Primary assembly: short summary",
                     "output_name": "busco_sum",
@@ -1993,15 +2013,15 @@
             "uuid": "0496de4b-ec62-48d5-8c36-e2f946ca728d",
             "when": null,
             "workflow_outputs": [
-                {
-                    "label": "Read Coverage and cutoffs calculation on alternate assembly : Histogram Plot",
-                    "output_name": "hist",
-                    "uuid": "f12c1cc7-a12a-4314-ae16-2738b80afe70"
-                },
                 {
                     "label": "Cutoffs for alternate assembly",
                     "output_name": "calcuts_cutoff",
                     "uuid": "49bf0c95-0290-4f8b-a9d7-2f17f53e9d26"
+                },
+                {
+                    "label": "Read Coverage and cutoffs calculation on alternate assembly : Histogram Plot",
+                    "output_name": "hist",
+                    "uuid": "f12c1cc7-a12a-4314-ae16-2738b80afe70"
                 }
             ]
         },
@@ -2399,6 +2419,13 @@
                     "action_type": "TagDatasetAction",
                     "output_name": "bed_files"
                 },
+                "TagDatasetActionhist_files": {
+                    "action_arguments": {
+                        "tags": "name:p,merqury_p_gff"
+                    },
+                    "action_type": "TagDatasetAction",
+                    "output_name": "hist_files"
+                },
                 "TagDatasetActionpng_files": {
                     "action_arguments": {
                         "tags": "merqury_p_png, #p"
@@ -2449,14 +2476,19 @@
             "when": null,
             "workflow_outputs": [
                 {
-                    "label": "Merqury on Phased assemblies: stats",
-                    "output_name": "stats_files",
-                    "uuid": "70f44477-6a3b-4ac4-b01a-f812ea880bae"
+                    "label": "Merqury on Phased assemblies: Gff",
+                    "output_name": "hist_files",
+                    "uuid": "bc07fbdf-b57c-4e11-a03b-5693741b3b4b"
                 },
                 {
                     "label": "Merqury on Phased assemblies: Images",
                     "output_name": "png_files",
                     "uuid": "ff9cfc96-449e-41d8-9c10-7f586ab6f479"
+                },
+                {
+                    "label": "Merqury on Phased assemblies: stats",
+                    "output_name": "stats_files",
+                    "uuid": "70f44477-6a3b-4ac4-b01a-f812ea880bae"
                 }
             ]
         },
@@ -3543,6 +3575,6 @@
     "tags": [
         "VGP_curated"
     ],
-    "uuid": "6b1b52f2-833c-4532-95c0-c85bc238fc76",
-    "version": 1
+    "uuid": "3b1b0946-90db-441b-9d76-5b9b123e5ef6",
+    "version": 2
 }