From 6ea1e6f4ee52ab2a4b8d686ffa722634ed9e8fe5 Mon Sep 17 00:00:00 2001
From: Delphine-L <lariviere.delphine@gmail.com>
Date: Wed, 9 Aug 2023 15:59:55 +0200
Subject: [PATCH] replacing the sorting tool by a faster one

---
 .../WF8a-Scaffolding_HiC_Yahs.ga              | 84 +++++++++++--------
 1 file changed, 50 insertions(+), 34 deletions(-)

diff --git a/workflows/VGP-assembly-v2/VGP-WF8a-Scaffolding_HiC_Yahs/WF8a-Scaffolding_HiC_Yahs.ga b/workflows/VGP-assembly-v2/VGP-WF8a-Scaffolding_HiC_Yahs/WF8a-Scaffolding_HiC_Yahs.ga
index 3298f82e0..1fe106f79 100644
--- a/workflows/VGP-assembly-v2/VGP-WF8a-Scaffolding_HiC_Yahs/WF8a-Scaffolding_HiC_Yahs.ga
+++ b/workflows/VGP-assembly-v2/VGP-WF8a-Scaffolding_HiC_Yahs/WF8a-Scaffolding_HiC_Yahs.ga
@@ -531,42 +531,53 @@
         },
         "14": {
             "annotation": "",
-            "content_id": "sort1",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
             "errors": null,
             "id": 14,
             "input_connections": {
-                "input": {
+                "infile": {
                     "id": 12,
                     "output_name": "output"
                 }
             },
-            "inputs": [],
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Sort",
+                    "name": "infile"
+                }
+            ],
             "label": null,
             "name": "Sort",
             "outputs": [
                 {
-                    "name": "out_file1",
+                    "name": "outfile",
                     "type": "input"
                 }
             ],
             "position": {
-                "left": 2165.9892497455858,
-                "top": 784.0625
+                "left": 2153.317301805489,
+                "top": 404.6762502767125
             },
             "post_job_actions": {
-                "TagDatasetActionout_file1": {
+                "TagDatasetActionoutfile": {
                     "action_arguments": {
                         "tags": "sorted_merged_alignments_s1"
                     },
                     "action_type": "TagDatasetAction",
-                    "output_name": "out_file1"
+                    "output_name": "outfile"
                 }
             },
-            "tool_id": "sort1",
-            "tool_state": "{\"column\": \"4\", \"column_set\": [], \"header_lines\": \"0\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"order\": \"ASC\", \"style\": \"alpha\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "1.2.0",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
+            "tool_shed_repository": {
+                "changeset_revision": "ddf54b12c295",
+                "name": "text_processing",
+                "owner": "bgruening",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
+            "tool_state": "{\"header\": \"0\", \"ignore_case\": false, \"infile\": {\"__class__\": \"RuntimeValue\"}, \"sortkeys\": [{\"__index__\": 0, \"column\": \"4\", \"order\": \"\", \"style\": \"\"}], \"unique\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "1.1.1",
             "type": "tool",
-            "uuid": "b888cd88-6df1-4252-9280-2f87510e2fe7",
+            "uuid": "2676952d-a894-4ddf-943a-71bed5fb8e9d",
             "when": null,
             "workflow_outputs": []
         },
@@ -634,7 +645,7 @@
                 },
                 "function|bfile": {
                     "id": 14,
-                    "output_name": "out_file1"
+                    "output_name": "outfile"
                 },
                 "function|enzyme_conditional|preconfigured_enzymes": {
                     "id": 4,
@@ -1964,50 +1975,55 @@
         },
         "34": {
             "annotation": "",
-            "content_id": "sort1",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
             "errors": null,
             "id": 34,
             "input_connections": {
-                "input": {
+                "infile": {
                     "id": 30,
                     "output_name": "output"
                 }
             },
-            "inputs": [],
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Sort",
+                    "name": "infile"
+                }
+            ],
             "label": null,
             "name": "Sort",
             "outputs": [
                 {
-                    "name": "out_file1",
+                    "name": "outfile",
                     "type": "input"
                 }
             ],
             "position": {
-                "left": 4562.332999745586,
-                "top": 530.921875
+                "left": 4553.075132770334,
+                "top": 390.1009386788954
             },
             "post_job_actions": {
-                "TagDatasetActionout_file1": {
+                "TagDatasetActionoutfile": {
                     "action_arguments": {
                         "tags": "sorted_merged_alignments_s2"
                     },
                     "action_type": "TagDatasetAction",
-                    "output_name": "out_file1"
+                    "output_name": "outfile"
                 }
             },
-            "tool_id": "sort1",
-            "tool_state": "{\"column\": \"4\", \"column_set\": [], \"header_lines\": \"0\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"order\": \"ASC\", \"style\": \"alpha\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "1.2.0",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
+            "tool_shed_repository": {
+                "changeset_revision": "ddf54b12c295",
+                "name": "text_processing",
+                "owner": "bgruening",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
+            "tool_state": "{\"header\": \"0\", \"ignore_case\": false, \"infile\": {\"__class__\": \"RuntimeValue\"}, \"sortkeys\": [{\"__index__\": 0, \"column\": \"4\", \"order\": \"\", \"style\": \"\"}], \"unique\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "1.1.1",
             "type": "tool",
-            "uuid": "3bcb0993-cf79-43c7-a7f7-d32ca0a93d06",
+            "uuid": "ae24a59d-8fc5-438b-9b96-3bec97bc41cd",
             "when": null,
-            "workflow_outputs": [
-                {
-                    "label": null,
-                    "output_name": "out_file1",
-                    "uuid": "6a5ce91b-1f23-4530-a69f-d0512c8cf4b0"
-                }
-            ]
+            "workflow_outputs": []
         },
         "35": {
             "annotation": "",
@@ -2060,6 +2076,6 @@
     "tags": [
         "VGP_curated"
     ],
-    "uuid": "34f82969-bab7-4939-a170-1b2d68a2deac",
-    "version": 2
+    "uuid": "6af34c00-c3e8-4fd9-954e-863ae47f4e20",
+    "version": 3
 }
\ No newline at end of file