From a28b9076bc73ab8b1e53964bdb5690efbfecbd96 Mon Sep 17 00:00:00 2001 From: Patrik Smeds Date: Mon, 28 Oct 2024 10:00:53 -0400 Subject: [PATCH] feat: updated version of pretext workflow developed by Delphine that takes HiFi and HiC as input. --- .../PretextMap_Generation.ga | 1425 +++++++++++++++++ 1 file changed, 1425 insertions(+) create mode 100644 workflows/VGP-assembly-v2/Curation-TreeValGal/PretextMap_Generation.ga diff --git a/workflows/VGP-assembly-v2/Curation-TreeValGal/PretextMap_Generation.ga b/workflows/VGP-assembly-v2/Curation-TreeValGal/PretextMap_Generation.ga new file mode 100644 index 0000000000..6f7328a999 --- /dev/null +++ b/workflows/VGP-assembly-v2/Curation-TreeValGal/PretextMap_Generation.ga @@ -0,0 +1,1425 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "", + "comments": [], + "format-version": "0.1", + "name": "PretextMap Generation with bed files (imported from URL)", + "report": { + "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n" + }, + "steps": { + "0": { + "annotation": "fasta file for haplotype 1", + "content_id": null, + "errors": null, + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "fasta file for haplotype 1", + "name": "haplotype 1" + } + ], + "label": "haplotype 1", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 3.027351459512147, + "top": 289.7673082139403 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"format\": [\"fasta\"], \"tag\": null}", + "tool_version": null, + "type": "data_input", + "uuid": "fa895dbf-8f06-4728-ac6c-d526fcff2578", + "when": null, + "workflow_outputs": [] + }, + "1": { + "annotation": "add haplotype suffic to contig names", + "content_id": null, + "errors": null, + "id": 1, + "input_connections": {}, + "inputs": [ + { + "description": "add haplotype suffic to contig names", + "name": "add haplotype suffix" + } + ], + "label": "add haplotype suffix", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 0.0, + "top": 370.5333251953125 + }, + "tool_id": null, + "tool_state": "{\"default\": true, \"parameter_type\": \"boolean\", \"optional\": true}", + "tool_version": null, + "type": "parameter_input", + "uuid": "742c987a-a4b8-4208-918a-cfb4bd55cd66", + "when": null, + "workflow_outputs": [] + }, + "2": { + "annotation": "fasta file for haplotype 2\n", + "content_id": null, + "errors": null, + "id": 2, + "input_connections": {}, + "inputs": [ + { + "description": "fasta file for haplotype 2\n", + "name": "haplotype 2" + } + ], + "label": "haplotype 2", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 1.11669921875, + "top": 468.23260556053623 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"format\": [\"fasta\"], \"tag\": null}", + "tool_version": null, + "type": "data_input", + "uuid": "b6516e91-ade5-457d-9b65-d54448413a13", + "when": null, + "workflow_outputs": [] + }, + "3": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 3, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Do you want to trim the Hi-C data?" + } + ], + "label": "Do you want to trim the Hi-C data?", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 687.5333251953125, + "top": 441.45001220703125 + }, + "tool_id": null, + "tool_state": "{\"default\": false, \"parameter_type\": \"boolean\", \"optional\": true}", + "tool_version": null, + "type": "parameter_input", + "uuid": "6d1391db-7fef-4b5c-a236-26016d6d0aab", + "when": null, + "workflow_outputs": [] + }, + "4": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 4, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "HiC reads - 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