diff --git a/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/CHANGELOG.md b/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/CHANGELOG.md index dabfdc5f30..a4c3b2d409 100644 --- a/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/CHANGELOG.md +++ b/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/CHANGELOG.md @@ -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 diff --git a/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/kmer-profiling-hifi-VGP1.ga b/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/kmer-profiling-hifi-VGP1.ga index 481a3f9a45..a1bd9a0363 100644 --- a/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/kmer-profiling-hifi-VGP1.ga +++ b/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/kmer-profiling-hifi-VGP1.ga @@ -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" @@ -315,7 +314,7 @@ }, "1": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mash_sketch/mash_sketch/2.3+galaxy2", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mash_sketch/mash_sketch/2.3+galaxy3", "errors": null, "id": 1, "input_connections": { @@ -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, @@ -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" @@ -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" @@ -551,7 +550,7 @@ }, "6": { "annotation": "", - "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": { @@ -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, @@ -647,7 +646,7 @@ } }, "tags": [], - "uuid": "a48248b3-838a-4b9e-a7e9-f8077694eceb" + "uuid": "15e8f353-8048-4db7-be96-b9bff1375909" }, "tool_id": null, "type": "subworkflow", @@ -681,7 +680,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Meryl", + "name": "options_kmer_size" + } + ], "label": null, "name": "Meryl", "outputs": [ @@ -1241,7 +1245,7 @@ } }, "tags": [], - "uuid": "73f0a313-62a7-4340-b351-30f41ad5f81c" + "uuid": "fa803730-b04a-46e5-a2e5-29910f19d795" }, "tool_id": null, "type": "subworkflow", @@ -1554,7 +1558,7 @@ } }, "tags": [], - "uuid": "4be37eef-5e0c-4153-afc3-5a1afc5a72a7" + "uuid": "ce34f1f1-02d9-4d5d-a03d-ef9709a9693d" }, "tool_id": null, "type": "subworkflow", @@ -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": [ @@ -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" } \ No newline at end of file