Updating workflows/amplicon/amplicon-mgnify/mgnify-amplicon-pipeline-v5-quality-control-single-end from 0.3 to 0.4

Author: planemo-autoupdate

workflows/amplicon/amplicon-mgnify/mgnify-amplicon-pipeline-v5-quality-control-single-end/CHANGELOG.md

@@ -1,5 +1,11 @@
 # Changelog
 
+## [0.4] - 2025-10-13
+
+### Automatic update
+- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy2`
+- `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy3` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy4`
+
 ## [0.3] - 2025-03-10
 
 ### Automatic update

workflows/amplicon/amplicon-mgnify/mgnify-amplicon-pipeline-v5-quality-control-single-end/mgnify-amplicon-pipeline-v5-quality-control-single-end.ga

@@ -24,7 +24,6 @@
     "format-version": "0.1",
     "license": "Apache-2.0",
     "name": "MGnify's amplicon pipeline v5.0 - Quality control SE",
-    "release": "0.3",
     "report": {
         "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
     },
@@ -49,7 +48,7 @@
                 "top": 219.5
             },
             "tool_id": null,
-            "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}",
+            "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\", \"fields\": null}",
             "tool_version": null,
             "type": "data_collection_input",
             "uuid": "743430cc-e893-4211-9107-663adf3b28b4",
@@ -391,7 +390,7 @@
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@@ -420,15 +419,15 @@
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                 }
             },
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy0",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy2",
             "tool_shed_repository": {
-                "changeset_revision": "3dc70b59608c",
+                "changeset_revision": "c41d78ae5fee",
                 "name": "text_processing",
                 "owner": "bgruening",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
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-            "tool_version": "9.5+galaxy0",
+            "tool_version": "9.5+galaxy2",
             "type": "tool",
             "uuid": "93d70102-188c-4c9e-b0b4-fcb24acd8a28",
             "when": null,
@@ -682,7 +681,7 @@
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             "annotation": "",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy0",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy2",
             "errors": null,
             "id": 15,
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@@ -711,15 +710,15 @@
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-            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy0",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy2",
             "tool_shed_repository": {
-                "changeset_revision": "3dc70b59608c",
+                "changeset_revision": "c41d78ae5fee",
                 "name": "text_processing",
                 "owner": "bgruening",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
             "tool_state": "{\"find_and_replace\": [{\"__index__\": 0, \"find_pattern\": \"\\\\t(.*?)\\\\.gz\", \"replace_pattern\": \"\\\\t$1_trimming\", \"is_regex\": true, \"global\": true, \"caseinsensitive\": false, \"wholewords\": false, \"skip_first_line\": false, \"searchwhere\": {\"searchwhere_select\": \"line\", \"__current_case__\": 0}}], \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "9.5+galaxy0",
+            "tool_version": "9.5+galaxy2",
             "type": "tool",
             "uuid": "687e1130-33fc-4890-8099-e2c6da98f836",
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@@ -839,7 +838,7 @@
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         "18": {
             "annotation": "",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy0",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy2",
             "errors": null,
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@@ -868,15 +867,15 @@
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                 }
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-            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy0",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy2",
             "tool_shed_repository": {
-                "changeset_revision": "3dc70b59608c",
+                "changeset_revision": "c41d78ae5fee",
                 "name": "text_processing",
                 "owner": "bgruening",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
             "tool_state": "{\"find_and_replace\": [{\"__index__\": 0, \"find_pattern\": \"\\\\t(.*?)\\\\.gz\", \"replace_pattern\": \"\\\\t$1_length_filtering\", \"is_regex\": true, \"global\": true, \"caseinsensitive\": false, \"wholewords\": false, \"skip_first_line\": false, \"searchwhere\": {\"searchwhere_select\": \"line\", \"__current_case__\": 0}}], \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "9.5+galaxy0",
+            "tool_version": "9.5+galaxy2",
             "type": "tool",
             "uuid": "1650ae45-7ee2-4765-8953-48a6548b1c67",
             "when": null,
@@ -917,7 +916,7 @@
             },
             "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_formatter/cshl_fasta_formatter/1.0.1+galaxy2",
             "tool_shed_repository": {
-                "changeset_revision": "516b97a23d7e",
+                "changeset_revision": "e773f1eb16cf",
                 "name": "fasta_formatter",
                 "owner": "devteam",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
@@ -937,7 +936,7 @@
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         "20": {
             "annotation": "",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy0",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy2",
             "errors": null,
             "id": 20,
             "input_connections": {
@@ -966,23 +965,23 @@
                     "output_name": "outfile"
                 }
             },
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy0",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy2",
             "tool_shed_repository": {
-                "changeset_revision": "3dc70b59608c",
+                "changeset_revision": "c41d78ae5fee",
                 "name": "text_processing",
                 "owner": "bgruening",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
             "tool_state": "{\"find_and_replace\": [{\"__index__\": 0, \"find_pattern\": \"\\\\t(.*?)\\\\.gz\", \"replace_pattern\": \"\\\\t$1_ambiguous_base_filtering\", \"is_regex\": true, \"global\": true, \"caseinsensitive\": false, \"wholewords\": false, \"skip_first_line\": false, \"searchwhere\": {\"searchwhere_select\": \"line\", \"__current_case__\": 0}}], \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "9.5+galaxy0",
+            "tool_version": "9.5+galaxy2",
             "type": "tool",
             "uuid": "284c9abf-2ebb-490c-a4d9-1fe997a1f562",
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             "workflow_outputs": []
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         "21": {
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-            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy3",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy4",
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@@ -1041,15 +1040,15 @@
                     "output_name": "stats"
                 }
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-            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy3",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy4",
             "tool_shed_repository": {
-                "changeset_revision": "31c42a2c02d3",
+                "changeset_revision": "e4dd4c0622f6",
                 "name": "multiqc",
                 "owner": "iuc",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
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-            "tool_version": "1.27+galaxy3",
+            "tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"image_content_input\": {\"__class__\": \"RuntimeValue\"}, \"png_plots\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"fastqc\", \"__current_case__\": 8, \"output\": [{\"__index__\": 0, \"type\": \"data\", \"input\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 1, \"type\": \"data\", \"input\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 2, \"type\": \"data\", \"input\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 3, \"type\": \"data\", \"input\": {\"__class__\": \"ConnectedValue\"}}]}}], \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "1.27+galaxy4",
             "type": "tool",
             "uuid": "640f4f45-c12a-47e0-846b-9b150ed8beca",
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@@ -1073,6 +1072,7 @@
         "metagenomics",
         "name:microgalaxy"
     ],
-    "uuid": "68bf2a73-d68a-4e25-ba52-5586c057df77",
-    "version": 20
+    "uuid": "6855a2e5-43db-4249-9585-425b59bf18b0",
+    "version": 1,
+    "release": "0.4"
 }