diff --git a/workflows/genome-assembly/bacterial-genome-assembly/CHANGELOG.md b/workflows/genome-assembly/bacterial-genome-assembly/CHANGELOG.md index cb5a34c219..b2b225052a 100644 --- a/workflows/genome-assembly/bacterial-genome-assembly/CHANGELOG.md +++ b/workflows/genome-assembly/bacterial-genome-assembly/CHANGELOG.md @@ -1,5 +1,10 @@ # Changelog +## [2.0.2] - 2025-12-22 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.1.0+galaxy2` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.4.2+galaxy0` + ## [2.0.1] - 2025-12-01 ### Automatic update diff --git a/workflows/genome-assembly/bacterial-genome-assembly/bacterial_genome_assembly.ga b/workflows/genome-assembly/bacterial-genome-assembly/bacterial_genome_assembly.ga index 71ce05c1ae..7c47565414 100644 --- a/workflows/genome-assembly/bacterial-genome-assembly/bacterial_genome_assembly.ga +++ b/workflows/genome-assembly/bacterial-genome-assembly/bacterial_genome_assembly.ga @@ -94,7 +94,7 @@ }, "2": { "annotation": "genome assembly with shovill tool", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.1.0+galaxy2", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.4.2+galaxy0", "errors": null, "id": 2, "input_connections": { @@ -206,15 +206,16 @@ "output_name": "shovill_std_log" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.1.0+galaxy2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.4.2+galaxy0", "tool_shed_repository": { - "changeset_revision": "ee17a294d3a3", + "changeset_revision": "331109486d58", "name": "shovill", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"adv\": {\"namefmt\": \"contig%05d\", \"depth\": \"100\", \"gsize\": \"\", \"kmers\": \"\", \"opts\": \"\", \"keep_files\": {\"nocorr\": \"yes_correction\", \"__current_case__\": 1, \"keepfiles\": true}, \"minlen\": \"0\", \"mincov\": \"2\"}, \"assembler\": \"spades\", \"library\": {\"lib_type\": \"paired\", \"__current_case__\": 0, \"R1\": {\"__class__\": \"ConnectedValue\"}, \"R2\": {\"__class__\": \"ConnectedValue\"}}, \"log\": true, \"trim\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.1.0+galaxy2", + "tool_state": "{\"adv\": {\"namefmt\": \"contig%05d\", \"depth\": \"100\", \"gsize\": \"\", \"kmers\": \"\", \"opts\": \"\", \"keep_files\": {\"nocorr\": \"yes_correction\", \"__current_case__\": 1, \"keepfiles\": true}, \"minlen\": \"0\", \"mincov\": \"2\"}, \"assembler\": \"spades\", \"assembler_type\": {\"assembler\": \"spades\", \"__current_case__\": 3, \"plasmid\": false}, \"library\": {\"lib_type\": \"paired\", \"__current_case__\": 0, \"R1\": {\"__class__\": \"ConnectedValue\"}, \"R2\": {\"__class__\": \"ConnectedValue\"}}, \"log\": true, \"trim\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "1.4.2+galaxy0", "type": "tool", "uuid": "e7b73002-c415-445b-9e00-51f45caefe88", "when": null, @@ -289,6 +290,7 @@ "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"tsv\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, "tool_version": "2022.09+galaxy2", "type": "tool", "uuid": "9a92c323-4df3-4cb7-8ca6-abdf73de0ff3", @@ -349,6 +351,7 @@ "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"fontsize\": null, \"height\": \"1000\", \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"lengths\": false, \"names\": false, \"nodewidth\": null, \"output_format\": \"svg\", \"width\": \"1000\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, "tool_version": "2022.09+galaxy4", "type": "tool", "uuid": "4482449a-7009-475d-9095-5d08fd465fed", @@ -408,7 +411,8 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"log\": false, \"tool_section\": {\"tools\": [{\"__index__\": 0, \"select_tool\": {\"tool_list\": \"shovill\", \"__current_case__\": 36, \"input\": {\"__class__\": \"RuntimeValue\"}, \"contig_graph_path\": {\"__class__\": \"RuntimeValue\"}, \"bam_file_path\": {\"__class__\": \"RuntimeValue\"}, \"origin\": {\"origin\": \"false\", \"__current_case__\": 1}, \"reference_database_version\": null}}]}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"log\": false, \"tool_section\": {\"tools\": [{\"__index__\": 0, \"select_tool\": {\"tool_list\": \"shovill\", \"__current_case__\": 36, \"input\": {\"__class__\": \"ConnectedValue\"}, \"contig_graph_path\": {\"__class__\": \"RuntimeValue\"}, \"bam_file_path\": {\"__class__\": \"RuntimeValue\"}, \"origin\": {\"origin\": \"false\", \"__current_case__\": 1}, \"reference_database_version\": null}}]}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, "tool_version": "1.0.4+galaxy0", "type": "tool", "uuid": "12e27969-f4a9-47c8-a561-d7145ac83a0a", @@ -432,12 +436,7 @@ "output_name": "output_json" } }, - "inputs": [ - { - "description": "runtime parameter for tool ToolDistillator Summarize", - "name": "summarize_data" - } - ], + "inputs": [], "label": "ToolDistillator summarize", "name": "ToolDistillator Summarize", "outputs": [ @@ -473,7 +472,8 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"summarize_data\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"summarize_data\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, "tool_version": "1.0.4+galaxy0", "type": "tool", "uuid": "e12a9c8d-3bf6-4f7e-8007-ba25d5722ce2", @@ -496,7 +496,7 @@ "quality", "ABRomics" ], - "uuid": "14fc2baa-a9fb-4e90-a8ec-f542faf1d8c2", + "uuid": "9737065e-678c-4073-b20e-e40077e80dcd", "version": 1, - "release": "2.0.1" + "release": "2.0.2" } \ No newline at end of file