diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/Assembly-Hifi-Trio-phasing-VGP5.ga b/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/Assembly-Hifi-Trio-phasing-VGP5.ga index 6a229c06a5..478dc0118a 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/Assembly-Hifi-Trio-phasing-VGP5.ga +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/Assembly-Hifi-Trio-phasing-VGP5.ga @@ -592,7 +592,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Cutadapt", + "name": "library" + } + ], "label": null, "name": "Cutadapt", "outputs": [ @@ -875,7 +880,7 @@ }, "25": { "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": 25, "input_connections": { @@ -884,7 +889,12 @@ "output_name": "report" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool MultiQC", + "name": "image_content_input" + } + ], "label": null, "name": "MultiQC", "outputs": [ @@ -902,15 +912,15 @@ "top": 236.97660611127793 }, "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\": \"\", \"export\": false, \"flat\": false, \"image_content_input\": {\"__class__\": \"RuntimeValue\"}, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"cutadapt\", \"__current_case__\": 5, \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"saveLog\": \"false\", \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "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\": \"cutadapt\", \"__current_case__\": 5, \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"saveLog\": \"false\", \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.27+galaxy4", "type": "tool", "uuid": "b64b5b58-cf21-4fb6-af57-2e8a56e85142", "when": null, @@ -1210,7 +1220,20 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Hifiasm", + "name": "assembly_options" + }, + { + "description": "runtime parameter for tool Hifiasm", + "name": "mode" + }, + { + "description": "runtime parameter for tool Hifiasm", + "name": "mode" + } + ], "label": null, "name": "Hifiasm", "outputs": [ @@ -1370,7 +1393,12 @@ "output_name": "hap1_contigs" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "mode_condition" + } + ], "label": null, "name": "gfastats", "outputs": [ @@ -1430,7 +1458,12 @@ "output_name": "hap2_contigs" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "mode_condition" + } + ], "label": "No Sequence hap2 gfa", "name": "gfastats", "outputs": [ @@ -1543,7 +1576,12 @@ "output_name": "hap1_contigs" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "mode_condition" + } + ], "label": "No Sequence hap1 gfa", "name": "gfastats", "outputs": [ @@ -1603,7 +1641,12 @@ "output_name": "hap2_contigs" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "mode_condition" + } + ], "label": null, "name": "gfastats", "outputs": [ @@ -1663,7 +1706,12 @@ "output_name": "hap1_contigs" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "mode_condition" + } + ], "label": null, "name": "gfastats", "outputs": [ @@ -1737,7 +1785,12 @@ "output_name": "hap2_contigs" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "mode_condition" + } + ], "label": null, "name": "gfastats", "outputs": [ @@ -1998,7 +2051,7 @@ }, "45": { "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": 45, "input_connections": { @@ -2015,7 +2068,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Busco", + "name": "lineage" + } + ], "label": "Busco Hap1", "name": "Busco", "outputs": [ @@ -2081,15 +2139,15 @@ "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": "bc06da8e-e5cb-493e-98d1-c974a3e46cff", "when": null, @@ -2250,7 +2308,7 @@ }, "47": { "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": 47, "input_connections": { @@ -2267,7 +2325,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Busco", + "name": "lineage" + } + ], "label": "Busco Hap2", "name": "Busco", "outputs": [ @@ -2333,15 +2396,15 @@ "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": "4931c626-b636-43c3-b19b-3c778199b9a8", "when": null, @@ -2527,7 +2590,20 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Merqury", + "name": "mode" + }, + { + "description": "runtime parameter for tool Merqury", + "name": "mode" + }, + { + "description": "runtime parameter for tool Merqury", + "name": "mode" + } + ], "label": null, "name": "Merqury", "outputs": [ @@ -3028,7 +3104,7 @@ } }, "tags": [], - "uuid": "3e40f4bd-3ee0-4ee2-8365-e0a75d34b2a9" + "uuid": "e035541b-bf99-484a-ad67-262278c505c4" }, "tool_id": null, "type": "subworkflow", @@ -3410,7 +3486,7 @@ } }, "tags": [], - "uuid": "0e393561-6d1e-4b70-a8e4-777e61bcdb65" + "uuid": "ba6d5bf9-7530-48c4-8e2a-465a7df90b33" }, "tool_id": null, "type": "subworkflow", @@ -4293,7 +4369,7 @@ } }, "tags": [], - "uuid": "d9d92f65-8323-465d-a83d-eb70657e0a0c" + "uuid": "0595db49-9311-451c-822d-563c8c06e506" }, "tool_id": null, "type": "subworkflow", @@ -4471,7 +4547,7 @@ "VGP", "Reviewed" ], - "uuid": "9fc9042f-6171-451a-bdd7-010abdb5b683", + "uuid": "b83ce482-7122-4387-a87b-e529c4a41ef0", "version": 1, - "release": "0.9.9" -} + "release": "0.9.10" +} \ No newline at end of file diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/CHANGELOG.md b/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/CHANGELOG.md index 843a4e9563..baae70858c 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/CHANGELOG.md +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/CHANGELOG.md @@ -1,5 +1,11 @@ # Changelog +## [0.9.10] - 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` + ## [0.9.9] - 2025-09-29 ### Automatic update