From cd8a981a70eba835a210bddec6196b0124bb6ddd Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Wed, 20 Nov 2024 11:59:33 -0500 Subject: [PATCH] add precuration jbrowse generation workflow complementary to the pretextmap generation --- .../Pre-Curation_Jbrowse2/CHANGELOG.md | 5 + .../Precuration_Jbrowse2.ga | 1438 +++++++++++++++++ .../Pre-Curation_Jbrowse2/README.md | 20 + 3 files changed, 1463 insertions(+) create mode 100644 workflows/VGP-assembly-v2/Pre-Curation_Jbrowse2/CHANGELOG.md create mode 100644 workflows/VGP-assembly-v2/Pre-Curation_Jbrowse2/Precuration_Jbrowse2.ga create mode 100644 workflows/VGP-assembly-v2/Pre-Curation_Jbrowse2/README.md diff --git a/workflows/VGP-assembly-v2/Pre-Curation_Jbrowse2/CHANGELOG.md b/workflows/VGP-assembly-v2/Pre-Curation_Jbrowse2/CHANGELOG.md new file mode 100644 index 000000000..b1f0d0644 --- /dev/null +++ b/workflows/VGP-assembly-v2/Pre-Curation_Jbrowse2/CHANGELOG.md @@ -0,0 +1,5 @@ +# Changelog + +## [1.0] 2024-11-20 + +- Creation of a workflow for the generation of a JBrowse2 instance with coverage, gaps and Telomere Tracks, as well as syntenic dotplots for related species. \ No newline at end of file diff --git a/workflows/VGP-assembly-v2/Pre-Curation_Jbrowse2/Precuration_Jbrowse2.ga b/workflows/VGP-assembly-v2/Pre-Curation_Jbrowse2/Precuration_Jbrowse2.ga new file mode 100644 index 000000000..d3273b728 --- /dev/null +++ b/workflows/VGP-assembly-v2/Pre-Curation_Jbrowse2/Precuration_Jbrowse2.ga @@ -0,0 +1,1438 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "", + "comments": [ + { + "child_steps": [ + 8, + 11 + ], + "color": "blue", + "data": { + "title": "Generate syntenic dotplots" + }, + "id": 1, + "position": [ + 758.5, + 601 + ], + "size": [ + 590, + 598 + ], + "type": "frame" + }, + { + "child_steps": [ + 14, + 15 + ], + "color": "turquoise", + "data": { + "title": "Jbrowse 2 Instance Creation" + }, + "id": 2, + "position": [ + 1703.6, + 52.9 + ], + "size": [ + 773, + 1207 + ], + "type": "frame" + }, + { + "child_steps": [ + 7, + 9, + 10, + 12, + 13 + ], + "color": "green", + "data": { + "title": "Convert gaps from features to histogram" + }, + "id": 0, + "position": [ + 460.2, + 0 + ], + "size": [ + 1163, + 540 + ], + "type": "frame" + } + ], + "creator": [ + { + "class": "Person", + "identifier": "", + "name": "Ross Lazarus" + }, + { + "class": "Person", + "identifier": "anna.syme@gmail.com", + "name": "Anna Syme" + }, + { + "class": "Person", + "identifier": "nadibraj@gmail.com", + "name": "Nadolina Brajuka" + }, + { + "class": "Person", + "identifier": "lariviere.delphine@gmail.com", + "name": "Delphine Lariviere" + } + ], + "format-version": "0.1", + "license": "MIT", + "release": "1.0", + "name": "Precuration - Jbrowse2", + "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": "This will be the sequence, divided into individual fasta contigs, on which tracks are arranged and displayed.", + "content_id": null, + "errors": null, + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "This will be the sequence, divided into individual fasta contigs, on which tracks are arranged and displayed.", + "name": "Genome assembly to report on" + } + ], + "label": "Genome assembly to report on", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 0, + "top": 65.23426933172311 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"tag\": null}", + "tool_version": null, + "type": "data_input", + "uuid": "faf8a4ed-0b0f-4b8f-8215-49aef8f97e30", + "when": null, + "workflow_outputs": [] + }, + "1": { + "annotation": "The wiggles are all smoothed by measuring over a window with default of 50 bases. 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\"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.15.4+galaxy7", + "type": "tool", + "uuid": "c7038bb0-799a-4bb0-baf0-495082e1ae27", + "when": null, + "workflow_outputs": [ + { + "label": "JBrowse2 for export", + "output_name": "output", + "uuid": "20b1ecd6-4931-4ad3-8054-feafd258066b" + } + ] + } + }, + "tags": [], + "uuid": "75080402-8768-4ae2-9b97-95bd3d999483", + "version": 10 +} \ No newline at end of file diff --git a/workflows/VGP-assembly-v2/Pre-Curation_Jbrowse2/README.md b/workflows/VGP-assembly-v2/Pre-Curation_Jbrowse2/README.md new file mode 100644 index 000000000..2a80fd0ec --- /dev/null +++ b/workflows/VGP-assembly-v2/Pre-Curation_Jbrowse2/README.md @@ -0,0 +1,20 @@ +# JBrowse2 instance generation + +This workflow generates a JBrowse 2 instance for a genome assembly. It is meant to be run after the Pre-curation workflow generating the PretextMaps files. . It includes tracks for PacBio read coverage, Gaps, telomeres, and syntenic dotplots for related species. + + +## Inputs + +1. **Genome assembly to report on** [fasta] The concatenated haplotypes Generated by the Pre-curation PretextMap workflow +2. **Window size for bed to bigwig - 50 default** The window size use to display the coverage and gaps density +3. Telomere bed file [bed] Output of seqtk_telo in the Pre-curation PretextMap workflow +4. Coverage bigwig [bigwig] Output of bamcoverage in the Pre-curation PretextMap workflow +5. Gaps bed [bed] Output of gfastats in the Pre-curation PretextMap workflow +6. **Will you provide a collection of related species for sequence similarity mapping?** If *yes*, provide the next input +7. **Collection of related species** [fasta] Collection containing the genomic sequences of closely related species + + +## Outputs + +1. JBrowse2 For Viewing : click on the eye to display the instance in Galaxy +2. JBrowse2 for export : zip file for download of export. \ No newline at end of file