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Updating workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4 from 0.3.13 to 0.3.14 #965

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Updating workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4 from 0.3.13 to 0.3.14 #965

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134 changes: 108 additions & 26 deletions workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4.ga
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Expand Up @@ -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"
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"output_name": "output"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool Cutadapt",
"name": "library"
}
],
"label": null,
"name": "Cutadapt",
"outputs": [
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"output_name": "output"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool Cutadapt",
"name": "library"
}
],
"label": null,
"name": "Cutadapt",
"outputs": [
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},
"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": {
Expand All @@ -785,7 +794,12 @@
"output_name": "report"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool MultiQC",
"name": "image_content_input"
}
],
"label": null,
"name": "MultiQC",
"outputs": [
Expand All @@ -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,
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"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": [
Expand Down Expand Up @@ -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": [
Expand Down Expand Up @@ -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": [
Expand Down Expand Up @@ -1325,7 +1354,7 @@
}
},
"tags": [],
"uuid": "e588a4b9-e88f-4138-a3d6-d538c9f88d1b"
"uuid": "1f087458-b1bd-4abe-aa09-d5b1ab30984f"
},
"tool_id": null,
"type": "subworkflow",
Expand Down Expand Up @@ -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": [
Expand Down Expand Up @@ -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": [
Expand Down Expand Up @@ -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": [
Expand Down Expand Up @@ -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": [
Expand Down Expand Up @@ -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": [
Expand Down Expand Up @@ -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": [
Expand Down Expand Up @@ -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": [
Expand Down Expand Up @@ -3141,7 +3217,7 @@
}
},
"tags": [],
"uuid": "5cdf3f78-e2bb-4f21-8a59-6117798d35d4"
"uuid": "98d9ace5-59bd-4852-ab3c-2b7688920749"
},
"tool_id": null,
"type": "subworkflow",
Expand Down Expand Up @@ -3523,7 +3599,7 @@
}
},
"tags": [],
"uuid": "b82f7cc3-3776-44ee-aa7d-5d726b4cae98"
"uuid": "6e62f946-3023-4c5e-b493-a266c9669ca7"
},
"tool_id": null,
"type": "subworkflow",
Expand Down Expand Up @@ -4221,7 +4297,7 @@
}
},
"tags": [],
"uuid": "84bf21d6-b91d-491a-bafe-ab6be8ea5476"
"uuid": "4295d65d-909d-494d-82f1-4d91c9200d30"
},
"tool_id": null,
"type": "subworkflow",
Expand Down Expand Up @@ -4579,7 +4655,12 @@
"output_name": "output"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool Merqury",
"name": "mode"
}
],
"label": "Merqury",
"name": "Merqury",
"outputs": [
Expand Down Expand Up @@ -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"
}
5 changes: 5 additions & 0 deletions workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/CHANGELOG.md
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# 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
Expand Down
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