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Updating workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1 from 0.5 to 0.6 #981

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Updating workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1 from 0.5 to 0.6 #981

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6 changes: 6 additions & 0 deletions workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/CHANGELOG.md
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@@ -1,5 +1,11 @@
# Changelog

## [0.6] - 2025-10-20

### Automatic update
- `toolshed.g2.bx.psu.edu/repos/iuc/mash_sketch/mash_sketch/2.3+galaxy2` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/mash_sketch/mash_sketch/2.3+galaxy3`
- `toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.1.3.1+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.2.0+galaxy1`

## [0.5] - 2025-10-01

# Changes
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50 changes: 32 additions & 18 deletions workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/kmer-profiling-hifi-VGP1.ga
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Expand Up @@ -15,7 +15,6 @@
],
"format-version": "0.1",
"license": "CC-BY-4.0",
"release": "0.5",
"name": "K-mer profiling and reads statistics VGP1",
"report": {
"markdown": "# Workflow 1: Kmer Profiling and reads statistics\n\nSpecies:\n\n```galaxy\nhistory_dataset_peek(output=\"Species for report\")\n```\n\nAssembly:\n\n```galaxy\nhistory_dataset_peek(output=\"Assembly for report\")\n```\n\nk-mer length:\n\n```galaxy\nhistory_dataset_peek(output=\"K-mer length for report\")\n```\n\n## GenomeScope results\n\nEstimated Genome Size\n\n\r\n```galaxy\nhistory_dataset_peek(output=\"Est_size_param\")\n```\r\n\n\nHomozygous read coverage:\n\n```galaxy\nhistory_dataset_peek(output=\"Homozygous Read Coverage\")\n```\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Montage Genomescope\")\n```\n\n## HiFi reads QC\n\n### Mash Dist\n\n\n```galaxy\nhistory_dataset_as_image(output=\"HeatMap\")\n```\n\n\n### Rdeval\n\n```galaxy\nhistory_dataset_as_table(output=\"Reads Statistics\")\n```\n\n\n\n"
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},
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"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mash_sketch/mash_sketch/2.3+galaxy2",
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"errors": null,
"id": 1,
"input_connections": {
Expand Down Expand Up @@ -344,15 +343,15 @@
"output_name": "sketch"
}
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mash_sketch/mash_sketch/2.3+galaxy2",
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mash_sketch/mash_sketch/2.3+galaxy3",
"tool_shed_repository": {
"changeset_revision": "3852f36e3154",
"changeset_revision": "9de5319ad2db",
"name": "mash_sketch",
"owner": "iuc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"kmer_size\": \"21\", \"prob_threshold\": \"0.01\", \"reads_assembly\": {\"reads_assembly_selector\": \"reads\", \"__current_case__\": 0, \"reads_input\": {\"reads_input_selector\": \"single\", \"__current_case__\": 1, \"reads\": {\"__class__\": \"ConnectedValue\"}}, \"minimum_kmer_copies\": \"1\", \"target_coverage\": null, \"genome_size\": null}, \"sketch_size\": \"1000\", \"__page__\": 0, \"__rerun_remap_job_id__\": null}",
"tool_version": "2.3+galaxy2",
"tool_version": "2.3+galaxy3",
"type": "tool",
"uuid": "c8a74dd7-3db4-42db-ad54-edb40c0415b6",
"when": null,
Expand Down Expand Up @@ -391,7 +390,7 @@
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mash_paste/mash_paste/2.3+galaxy0",
"tool_shed_repository": {
"changeset_revision": "8f32dcfde5d9",
"changeset_revision": "e0c0fda064eb",
"name": "mash_paste",
"owner": "iuc",
"tool_shed": "toolshed.g2.bx.psu.edu"
Expand Down Expand Up @@ -447,7 +446,7 @@
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mash_dist/mash_dist/2.3+galaxy0",
"tool_shed_repository": {
"changeset_revision": "8249e5aa200c",
"changeset_revision": "c932095af671",
"name": "mash_dist",
"owner": "iuc",
"tool_shed": "toolshed.g2.bx.psu.edu"
Expand Down Expand Up @@ -551,7 +550,7 @@
},
"6": {
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"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.1.3.1+galaxy0",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.2.0+galaxy1",
"errors": null,
"id": 6,
"input_connections": {
Expand All @@ -574,15 +573,15 @@
"top": 418.2968613301772
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.1.3.1+galaxy0",
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.2.0+galaxy1",
"tool_shed_repository": {
"changeset_revision": "374e9062d874",
"changeset_revision": "48b42ee61bc5",
"name": "ggplot2_heatmap2",
"owner": "iuc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"cluster_cond\": {\"cluster\": \"yes\", \"__current_case__\": 0, \"cluster_cols_rows\": \"both\", \"distance\": \"euclidean\", \"clustering\": \"complete\"}, \"colorchoice\": {\"type\": \"palettes\", \"__current_case__\": 0, \"name\": \"BrBG\"}, \"image_file_format\": \"png\", \"input1\": {\"__class__\": \"ConnectedValue\"}, \"key\": null, \"labels\": \"both\", \"title\": \"Mash Dist\", \"transform\": \"none\", \"zscore_cond\": {\"zscore\": \"none\", \"__current_case__\": 0, \"scale\": \"none\"}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}",
"tool_version": "3.1.3.1+galaxy0",
"tool_version": "3.2.0+galaxy1",
"type": "tool",
"uuid": "b3b450ca-b3bb-4fc4-888f-484da2f48487",
"when": null,
Expand Down Expand Up @@ -647,7 +646,7 @@
}
},
"tags": [],
"uuid": "a48248b3-838a-4b9e-a7e9-f8077694eceb"
"uuid": "15e8f353-8048-4db7-be96-b9bff1375909"
},
"tool_id": null,
"type": "subworkflow",
Expand Down Expand Up @@ -681,7 +680,12 @@
"output_name": "output"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool Meryl",
"name": "options_kmer_size"
}
],
"label": null,
"name": "Meryl",
"outputs": [
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}
},
"tags": [],
"uuid": "73f0a313-62a7-4340-b351-30f41ad5f81c"
"uuid": "fa803730-b04a-46e5-a2e5-29910f19d795"
},
"tool_id": null,
"type": "subworkflow",
Expand Down Expand Up @@ -1554,7 +1558,7 @@
}
},
"tags": [],
"uuid": "4be37eef-5e0c-4153-afc3-5a1afc5a72a7"
"uuid": "ce34f1f1-02d9-4d5d-a03d-ef9709a9693d"
},
"tool_id": null,
"type": "subworkflow",
Expand Down Expand Up @@ -1721,7 +1725,16 @@
"output_name": "output"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool rdeval",
"name": "input_filter"
},
{
"description": "runtime parameter for tool rdeval",
"name": "input_filter"
}
],
"label": "Rdeval Stats",
"name": "rdeval",
"outputs": [
Expand Down Expand Up @@ -1844,6 +1857,7 @@
"Reviewed",
"VGP"
],
"uuid": "f76c7eb0-71c7-4697-8fab-011eb7e4bcda",
"version": 10
"uuid": "43e56174-1b09-4c5c-830b-528671c137a4",
"version": 1,
"release": "0.6"
}