diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4.ga b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4.ga index 7ef82e5c66..cc3492f937 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4.ga +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4.ga @@ -20,7 +20,6 @@ ], "format-version": "0.1", "license": "CC-BY-4.0", - "release": "0.4", "name": "Genome Assembly from Hifi reads with HiC phasing - VGP4", "report": { "markdown": "\nSpecies\n\n\n```galaxy\nhistory_dataset_peek(output=\"Species Name for workflow report\")\n```\n\n\nAssembly\n\n```galaxy\nhistory_dataset_peek(output=\"Assembly Name for workflow report\")\n```\n\n\n## Raw unitig graph\n\n```galaxy\nhistory_dataset_as_image(output=\"raw unitig graph image\")\n```\n\n## Merqury results\n\n### Merqury QV\n\n```galaxy\nhistory_dataset_as_table(output=\"merqury_qv\")\n```\n\n### Merqury completeness\n\n```galaxy\nhistory_dataset_as_table(output=\"merqury_stats\")\n```\n\n### Merqury plots\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Merqury plot both haplotypes\")\n```\n\n```galaxy\nhistory_dataset_as_image(output=\"Merqury CN plots\")\n```\n\n\n\n## Compleasm results \n\nHap1\n\n```galaxy\nhistory_dataset_embedded(output=\"Compleasm on Contigs hap1 Summary\")\n```\n\n\nHap2\n```galaxy\nhistory_dataset_embedded(output=\"Compleasm on Contigs hap2 Summary\")\n```\n\n\n## Assembly statistics\n\n\n```galaxy\nhistory_dataset_as_table(output=\"clean_stats\")\n```\n\n\n## Nx and Size plots\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Montage Nx and size plots\")\n```\n\n\n\n\n## Current Workflow\n```galaxy\nworkflow_display()\n```\n" @@ -517,7 +516,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Cutadapt", + "name": "library" + } + ], "label": null, "name": "Cutadapt", "outputs": [ @@ -599,7 +603,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Cutadapt", + "name": "library" + } + ], "label": null, "name": "Cutadapt", "outputs": [ @@ -776,7 +785,7 @@ }, "21": { "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": 21, "input_connections": { @@ -785,7 +794,12 @@ "output_name": "report" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool MultiQC", + "name": "image_content_input" + } + ], "label": null, "name": "MultiQC", "outputs": [ @@ -803,15 +817,15 @@ "top": 337.54102155573605 }, "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": "c60d4342-a7fb-4dd1-8f5f-206fa7e423b8", "when": null, @@ -1181,7 +1195,12 @@ "output_name": "text_param" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Map parameter value", + "name": "input_param_type" + } + ], "label": null, "name": "Map parameter value", "outputs": [ @@ -1232,7 +1251,12 @@ "output_name": "text_param" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Map parameter value", + "name": "input_param_type" + } + ], "label": null, "name": "Map parameter value", "outputs": [ @@ -1283,7 +1307,12 @@ "output_name": "text_param" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Map parameter value", + "name": "input_param_type" + } + ], "label": null, "name": "Map parameter value", "outputs": [ @@ -1325,7 +1354,7 @@ } }, "tags": [], - "uuid": "e588a4b9-e88f-4138-a3d6-d538c9f88d1b" + "uuid": "1f087458-b1bd-4abe-aa09-d5b1ab30984f" }, "tool_id": null, "type": "subworkflow", @@ -1963,7 +1992,24 @@ "output_name": "out1" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Hifiasm", + "name": "assembly_options" + }, + { + "description": "runtime parameter for tool Hifiasm", + "name": "hic_partition" + }, + { + "description": "runtime parameter for tool Hifiasm", + "name": "hic_partition" + }, + { + "description": "runtime parameter for tool Hifiasm", + "name": "mode" + } + ], "label": "Hifiasm", "name": "Hifiasm", "outputs": [ @@ -2304,7 +2350,12 @@ "output_name": "hic_balanced_contig_hap2_graph" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "mode_condition" + } + ], "label": "gfastats gfa hap2 no sequences", "name": "gfastats", "outputs": [ @@ -2418,7 +2469,12 @@ "output_name": "hic_balanced_contig_hap1_graph" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "mode_condition" + } + ], "label": "gfastats gfa hap1", "name": "gfastats", "outputs": [ @@ -2478,7 +2534,12 @@ "output_name": "hic_balanced_contig_hap2_graph" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "mode_condition" + } + ], "label": "gfastats gfa hap2", "name": "gfastats", "outputs": [ @@ -2538,7 +2599,12 @@ "output_name": "hic_balanced_contig_hap2_graph" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "mode_condition" + } + ], "label": null, "name": "gfastats", "outputs": [ @@ -2583,7 +2649,12 @@ "output_name": "hic_balanced_contig_hap1_graph" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "mode_condition" + } + ], "label": "gfastats gfa hap1 no sequences", "name": "gfastats", "outputs": [ @@ -2643,7 +2714,12 @@ "output_name": "hic_balanced_contig_hap1_graph" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "mode_condition" + } + ], "label": null, "name": "gfastats", "outputs": [ @@ -3141,7 +3217,7 @@ } }, "tags": [], - "uuid": "5cdf3f78-e2bb-4f21-8a59-6117798d35d4" + "uuid": "98d9ace5-59bd-4852-ab3c-2b7688920749" }, "tool_id": null, "type": "subworkflow", @@ -3523,7 +3599,7 @@ } }, "tags": [], - "uuid": "b82f7cc3-3776-44ee-aa7d-5d726b4cae98" + "uuid": "6e62f946-3023-4c5e-b493-a266c9669ca7" }, "tool_id": null, "type": "subworkflow", @@ -4221,7 +4297,7 @@ } }, "tags": [], - "uuid": "84bf21d6-b91d-491a-bafe-ab6be8ea5476" + "uuid": "4295d65d-909d-494d-82f1-4d91c9200d30" }, "tool_id": null, "type": "subworkflow", @@ -4579,7 +4655,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Merqury", + "name": "mode" + } + ], "label": "Merqury", "name": "Merqury", "outputs": [ @@ -5449,6 +5530,7 @@ "VGP", "Reviewed" ], - "uuid": "f0ae78ab-8dc1-4807-b9c6-1efd8929ed6f", - "version": 25 + "uuid": "f5e1f912-9e0c-4ea7-98f3-8f0f85fc2efe", + "version": 1, + "release": "0.5" } \ No newline at end of file diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/CHANGELOG.md b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/CHANGELOG.md index 71a3ae0064..bcadf5995a 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/CHANGELOG.md +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/CHANGELOG.md @@ -1,5 +1,10 @@ # Changelog +## [0.5] - 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` + ## [0.4] - 2025-09-30 ### Changes