diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3.ga b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3.ga index b891d2ec74..f6c79e8633 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3.ga +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3.ga @@ -457,7 +457,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Cutadapt", + "name": "library" + } + ], "label": null, "name": "Cutadapt", "outputs": [ @@ -688,7 +693,7 @@ }, "19": { "annotation": "", - "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", "errors": null, "id": 19, "input_connections": { @@ -697,7 +702,12 @@ "output_name": "report" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool MultiQC", + "name": "image_content_input" + } + ], "label": null, "name": "MultiQC", "outputs": [ @@ -715,15 +725,15 @@ "top": 1052.86328125 }, "post_job_actions": {}, - "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" }, - "tool_state": "{\"comment\": {\"__class__\": \"ConnectedValue\"}, \"export\": false, \"flat\": false, \"image_content_input\": {\"__class__\": \"RuntimeValue\"}, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"cutadapt\", \"__current_case__\": 5, \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"title\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.27+galaxy3", + "tool_state": "{\"comment\": {\"__class__\": \"ConnectedValue\"}, \"export\": false, \"flat\": false, \"image_content_input\": {\"__class__\": \"RuntimeValue\"}, \"png_plots\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"cutadapt\", \"__current_case__\": 5, \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"title\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.27+galaxy4", "type": "tool", "uuid": "24ef7e9a-d7eb-4cda-8675-26e8ea167b54", "when": null, @@ -1067,7 +1077,16 @@ "output_name": "out1" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Hifiasm", + "name": "assembly_options" + }, + { + "description": "runtime parameter for tool Hifiasm", + "name": "mode" + } + ], "label": null, "name": "Hifiasm", "outputs": [ @@ -1226,7 +1245,12 @@ "output_name": "primary_contig_graph" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "mode_condition" + } + ], "label": null, "name": "gfastats", "outputs": [ @@ -1286,7 +1310,12 @@ "output_name": "primary_contig_graph" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "mode_condition" + } + ], "label": null, "name": "gfastats", "outputs": [ @@ -1346,7 +1375,12 @@ "output_name": "alternate_contig_graph" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "mode_condition" + } + ], "label": null, "name": "gfastats", "outputs": [ @@ -1406,7 +1440,12 @@ "output_name": "alternate_contig_graph" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "mode_condition" + } + ], "label": null, "name": "gfastats", "outputs": [ @@ -1466,7 +1505,12 @@ "output_name": "primary_contig_graph" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "mode_condition" + } + ], "label": null, "name": "gfastats", "outputs": [ @@ -1533,7 +1577,12 @@ "output_name": "alternate_contig_graph" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "mode_condition" + } + ], "label": null, "name": "gfastats", "outputs": [ @@ -1809,7 +1858,7 @@ }, "39": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy2", "errors": null, "id": 39, "input_connections": { @@ -1826,7 +1875,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Busco", + "name": "lineage" + } + ], "label": null, "name": "Busco", "outputs": [ @@ -1899,15 +1953,15 @@ "output_name": "summary_image" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy2", "tool_shed_repository": { - "changeset_revision": "4e70d88adf2f", + "changeset_revision": "c5a90fa4b8dd", "name": "busco", "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, \"use_augustus\": {\"use_augustus_selector\": \"metaeuk\", \"__current_case__\": 0}}, \"cached_db\": {\"__class__\": \"ConnectedValue\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage\": {\"lineage_mode\": \"select_lineage\", \"__current_case__\": 1, \"lineage_dataset\": {\"__class__\": \"ConnectedValue\"}}, \"outputs\": [\"short_summary\", \"missing\", \"image\", \"gff\"], \"test\": null, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", - "tool_version": "5.8.0+galaxy1", + "tool_version": "5.8.0+galaxy2", "type": "tool", "uuid": "1cd23635-275c-411f-b91d-f53f2bb229cb", "when": null, @@ -2080,7 +2134,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Merqury", + "name": "mode" + } + ], "label": null, "name": "Merqury", "outputs": [ @@ -2197,7 +2256,7 @@ }, "42": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy2", "errors": null, "id": 42, "input_connections": { @@ -2214,7 +2273,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Busco", + "name": "lineage" + } + ], "label": null, "name": "Busco", "outputs": [ @@ -2287,15 +2351,15 @@ "output_name": "summary_image" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy2", "tool_shed_repository": { - "changeset_revision": "4e70d88adf2f", + "changeset_revision": "c5a90fa4b8dd", "name": "busco", "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, \"use_augustus\": {\"use_augustus_selector\": \"metaeuk\", \"__current_case__\": 0}}, \"cached_db\": {\"__class__\": \"ConnectedValue\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage\": {\"lineage_mode\": \"select_lineage\", \"__current_case__\": 1, \"lineage_dataset\": {\"__class__\": \"ConnectedValue\"}}, \"outputs\": [\"short_summary\", \"missing\", \"image\", \"gff\"], \"test\": null, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", - "tool_version": "5.8.0+galaxy1", + "tool_version": "5.8.0+galaxy2", "type": "tool", "uuid": "bd6fc72e-8c57-4345-92c1-89d66d4d78b1", "when": null, @@ -2913,7 +2977,7 @@ } }, "tags": [], - "uuid": "4460df78-0760-4ffc-80fd-e7b5a952bade" + "uuid": "18a26c91-791d-41bb-bf8d-ba6c7280b705" }, "tool_id": null, "type": "subworkflow", @@ -3295,7 +3359,7 @@ } }, "tags": [], - "uuid": "8cb28c62-4367-4621-9dae-c2e886794385" + "uuid": "6ec87f96-c7dd-40d7-a1cd-3812a7e47ebe" }, "tool_id": null, "type": "subworkflow", @@ -4092,7 +4156,7 @@ } }, "tags": [], - "uuid": "0f75c5ff-d23c-4408-9a9d-6b1955c18d73" + "uuid": "1b46c5de-bf5b-4eb9-acb9-c50c2680cf96" }, "tool_id": null, "type": "subworkflow", @@ -4227,7 +4291,7 @@ "VGP", "Reviewed" ], - "uuid": "40ef3ef9-6781-42d6-baf0-70fe10cc9622", + "uuid": "5be7e9a2-d9b9-479c-907c-0e5249bf15da", "version": 1, - "release": "0.3.4" -} + "release": "0.3.5" +} \ No newline at end of file diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/CHANGELOG.md b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/CHANGELOG.md index 2ebf04960c..11d664901c 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/CHANGELOG.md +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/CHANGELOG.md @@ -1,5 +1,11 @@ # Changelog +## [0.3.5] - 2025-10-13 + +### Automatic update +- `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` +- `toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy2` + ## [0.3.4] - 2025-09-29 ### Automatic update