From c1b9f8c88ac0a131da71985ef9041e0015e7bdbd Mon Sep 17 00:00:00 2001 From: planemo-autoupdate Date: Mon, 24 Feb 2025 04:30:07 +0000 Subject: [PATCH 1/2] Updating workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5 from 0.7 to 0.8 --- .../Assembly-Hifi-Trio-phasing-VGP5.ga | 114 +++++++++++++++--- .../CHANGELOG.md | 5 + 2 files changed, 99 insertions(+), 20 deletions(-) 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 a752542cfb..4f30a4f8ae 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 @@ -15,7 +15,7 @@ ], "format-version": "0.1", "license": "CC-BY-4.0", - "release": "0.7", + "release": "0.8", "name": "Assembly-Hifi-Trio-phasing-VGP5", "report": { "markdown": "\n# Workflow Execution Report\n\nTime workflow was invoked:\n\n```galaxy\ninvocation_time()\n```\nGalaxy version :\n\n```galaxy\ngenerate_galaxy_version()\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_stats)\n```\n\n### Merqury completeness\n\n```galaxy\nhistory_dataset_as_table(output=\"merqury_stats\")\n```\n\n### Merqury plots\n\n\nspectra-cn:\n\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.spectra-cn.fl\")\n```\n\nspectra-asm:\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.spectra-asm.fl\")\n```\n\n\nhap1 spectra-cn:\n\n\r\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.assembly_01.spectra-cn.fl\")\n```\r\n\n\nhap2 spectra-cn:\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.assembly_02.spectra-cn.fl\")\n```\n\n## BUSCO results (Vertebrata database)\n\nHap1\n\n```galaxy\nhistory_dataset_as_image(output=\"Busco Summary Image Hap1\")\n```\n\nHap2\n\n```galaxy\nhistory_dataset_as_image(output=\"Busco Summary Image Hap2\")\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=\"Nx Plot\")\n```\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Size Plot\")\n```\n\n\n\n## Current Workflow\n```galaxy\nworkflow_display()\n```\n" @@ -464,7 +464,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Cutadapt", + "name": "library" + } + ], "label": null, "name": "Cutadapt", "outputs": [ @@ -696,7 +701,7 @@ }, "21": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy3", "errors": null, "id": 21, "input_connections": { @@ -705,7 +710,12 @@ "output_name": "report" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool MultiQC", + "name": "image_content_input" + } + ], "label": null, "name": "MultiQC", "outputs": [ @@ -723,15 +733,15 @@ "top": 79.2265625 }, "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy3", "tool_shed_repository": { - "changeset_revision": "d2aaac19f42f", + "changeset_revision": "31c42a2c02d3", "name": "multiqc", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": 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+galaxy1", + "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", "type": "tool", "uuid": "b64b5b58-cf21-4fb6-af57-2e8a56e85142", "when": null, @@ -1031,7 +1041,20 @@ "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": [ @@ -1191,7 +1214,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "mode_condition" + } + ], "label": null, "name": "gfastats", "outputs": [ @@ -1255,7 +1283,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "mode_condition" + } + ], "label": null, "name": "gfastats", "outputs": [ @@ -1372,7 +1405,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "mode_condition" + } + ], "label": null, "name": "gfastats", "outputs": [ @@ -1450,7 +1488,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "mode_condition" + } + ], "label": null, "name": "gfastats", "outputs": [ @@ -1728,7 +1771,16 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Busco", + "name": "lineage" + }, + { + "description": "runtime parameter for tool Busco", + "name": "lineage_conditional" + } + ], "label": null, "name": "Busco", "outputs": [ @@ -1843,7 +1895,16 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Busco", + "name": "lineage" + }, + { + "description": "runtime parameter for tool Busco", + "name": "lineage_conditional" + } + ], "label": null, "name": "Busco", "outputs": [ @@ -1966,7 +2027,20 @@ "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": [ @@ -2467,7 +2541,7 @@ } }, "tags": [], - "uuid": "e7ad70ed-bd55-4aa9-8d15-4270fcb26a4a" + "uuid": "990af8e2-a18e-48ae-892a-49aae5092106" }, "tool_id": null, "type": "subworkflow", @@ -2849,7 +2923,7 @@ } }, "tags": [], - "uuid": "4c500cfb-8a3b-4dae-a3d4-f9fe64c3ce67" + "uuid": "29af7a41-b2d8-4fba-aede-69a68ede37dd" }, "tool_id": null, "type": "subworkflow", @@ -3741,7 +3815,7 @@ } }, "tags": [], - "uuid": "731cd3ad-6798-4c4c-90bc-c0d8e640383f" + "uuid": "d8c8ce81-8cf6-40fb-8c13-d2357df044d9" }, "tool_id": null, "type": "subworkflow", @@ -3921,4 +3995,4 @@ ], "uuid": "bd09a130-801c-4cb8-b848-ab90b3161322", "version": 3 -} +} \ 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 c8a3a3a6a0..b58c59f747 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 +1,10 @@ # Changelog +## [0.8] 2025-02-24 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy3` + ## [0.7] 2025-02-17 ### Automatic update From d01b00f62a1d215bd90e9d6c8cc10082ad9d6380 Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Tue, 25 Feb 2025 11:33:23 -0500 Subject: [PATCH 2/2] remove runtime parameters --- .../Assembly-Hifi-Trio-phasing-VGP5.ga | 96 +++---------------- 1 file changed, 11 insertions(+), 85 deletions(-) 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 4f30a4f8ae..942c27858e 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 @@ -464,12 +464,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Cutadapt", - "name": "library" - } - ], + "inputs": [], "label": null, "name": "Cutadapt", "outputs": [ @@ -710,12 +705,7 @@ "output_name": "report" } }, - "inputs": [ - { - "description": "runtime parameter for tool MultiQC", - "name": "image_content_input" - } - ], + "inputs": [], "label": null, "name": "MultiQC", "outputs": [ @@ -1041,20 +1031,7 @@ "output_name": "output" } }, - "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" - } - ], + "inputs": [], "label": null, "name": "Hifiasm", "outputs": [ @@ -1214,12 +1191,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool gfastats", - "name": "mode_condition" - } - ], + "inputs": [], "label": null, "name": "gfastats", "outputs": [ @@ -1283,12 +1255,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool gfastats", - "name": "mode_condition" - } - ], + "inputs": [], "label": null, "name": "gfastats", "outputs": [ @@ -1405,12 +1372,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool gfastats", - "name": "mode_condition" - } - ], + "inputs": [], "label": null, "name": "gfastats", "outputs": [ @@ -1488,12 +1450,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool gfastats", - "name": "mode_condition" - } - ], + "inputs": [], "label": null, "name": "gfastats", "outputs": [ @@ -1771,16 +1728,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Busco", - "name": "lineage" - }, - { - "description": "runtime parameter for tool Busco", - "name": "lineage_conditional" - } - ], + "inputs": [], "label": null, "name": "Busco", "outputs": [ @@ -1895,16 +1843,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Busco", - "name": "lineage" - }, - { - "description": "runtime parameter for tool Busco", - "name": "lineage_conditional" - } - ], + "inputs": [], "label": null, "name": "Busco", "outputs": [ @@ -2027,20 +1966,7 @@ "output_name": "output" } }, - "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" - } - ], + "inputs": [], "label": null, "name": "Merqury", "outputs": [ @@ -3995,4 +3921,4 @@ ], "uuid": "bd09a130-801c-4cb8-b848-ab90b3161322", "version": 3 -} \ No newline at end of file +}