From a17289a8e950d0b8b691eb40c323380d1dd56e9d Mon Sep 17 00:00:00 2001 From: fubar2 Date: Wed, 9 Oct 2024 13:26:53 +1100 Subject: [PATCH] Push latest workflows to Delphine's fork --- .../Galaxy-Workflow-TreeValGalAugTwoHaps.ga | 7459 +++++++++++++++++ ...-Workflow-dimer_density_SV_and_coverage.ga | 4298 ++++++++++ 2 files changed, 11757 insertions(+) create mode 100644 workflows/VGP-assembly-v2/Curation-TreeValGal/Galaxy-Workflow-TreeValGalAugTwoHaps.ga create mode 100644 workflows/VGP-assembly-v2/Curation-TreeValGal/Galaxy-Workflow-dimer_density_SV_and_coverage.ga diff --git a/workflows/VGP-assembly-v2/Curation-TreeValGal/Galaxy-Workflow-TreeValGalAugTwoHaps.ga b/workflows/VGP-assembly-v2/Curation-TreeValGal/Galaxy-Workflow-TreeValGalAugTwoHaps.ga new file mode 100644 index 000000000..6fb06b38d --- /dev/null +++ b/workflows/VGP-assembly-v2/Curation-TreeValGal/Galaxy-Workflow-TreeValGalAugTwoHaps.ga @@ -0,0 +1,7459 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "Version of TreeValGal that always requires 2 haplotypes as input. One is displayed by default. Comparisons are easy because the other one's tracks are on the menu.\nTakes a collection of closely related species.\nThat part needs the fasta name attached to the contig names for PAF references because JBrowse2 cannot tell which PAF reference a hit in the second of the pair of matches came from :(", + "comments": [ + { + "color": "black", + "data": { + "text": "# Some random notes:\n\nUses Delphine's method for optional inputs.\n\nThe second JBrowse2 is a copy of the first but with the advanced option to write as a zip. \nTo update, only edit the first one. When done, copy it, set the output zip advanced option, then set the label and output name of the copy to include zip\n\nMashmap reference uses repeatmasker masked sequence to filter noise from low complexity element matches, and \"orthologous\" mapping for both haplotypes and related species. Not sure what's optimal. Advice appeciated\n\nJBrowse tracks can be off in the default view to make things less overwhelming. Need to open the track menu to see them. The independent haplotype paf tracks are hidden by default for example\n\nThe output reports on an assembly, optionally mat/pat haplotypes if contig names do not overlap - rubbish will be displayed if they do. With some pacbio reads, the main tracks can be produced. The annotation tracks require human choices for external genes and proteins, and comparison species for pafs.\n\nMashmap paf tracks are prepared for two comparison species references, and for an independent haplotype or refererence genome.\n\n\n# Choosing inputs for mashmap pafs:\n\n\nmashmap settings varied here are % identity and match length to cover a range since the evolutionary distances depend on the curator's choice of comparison organisms for some of them.\n\nAt this point, \"tuning\" for dotplots has aimed for a \"reasonable\" number of paf rows. Too many gets slow and dark. Too few and the patterns might be too faint to see clearly or when zoomed.\n\nNeed curator eyeballs and feedback for that.\n\nTwo different mashmap uses - for the selected related species sequence similarity patterns, and for independent haplotype or reference, if available\n\nThe 2 optional related species sequence similarity will depend on evolutionary distance. Discernable diagonal segments of mashmap hits become less likely - although they are seen with close relatives. \n\nThere are two mashmaps to give some spread but more could be added. Nice thing about TreeValGal workflow is that adding tracks is not at all difficult. Adding a wider range of parameters makes sense - particularly once the curators start looking at what they are getting?\n\nNeed to use the track menu for the main reference vs external reference/haplotype tracks - off by default.\n\nAgain there's a spread of 3 mashmap settings to get different numbers of hits - 20-40k seems to be a sweet spot for plots - more gets slower and clumsy but could be important if high resolution needed.\n\n# Annotation Fasta inputs:\n\nCurrently has 4 optional NCBI annotation tracks fasta - genes, cds, rna and one with the proteins - these are mapped with a specialised AA to nucleotide mapper so must be encoded as amino acids. Can be obtained with the appropriate species NCBI taxonId, as the taxon in the Galaxy NCBI gene annotation download tool.\n\n" + }, + "id": 2, + "position": [ + 0, + 1860 + ], + "size": [ + 1200, + 740 + ], + "type": "markdown" + }, + { + "child_steps": [ + 23, + 24, + 27, + 28, + 29, + 21, + 22, + 26 + ], + "color": "black", + "data": { + "title": "Basic reporting - repeats, telomeres, coverage and gaps" + }, + "id": 0, + "position": [ + 290, + 0 + ], + "size": [ + 1920, + 1060 + ], + "type": "frame" + }, + { + "child_steps": [ + 30, + 16, + 14, + 15, + 17, + 13, + 12, + 11, + 18 + ], + "color": "turquoise", + "data": { + "title": "Annotation fasta inputs" + }, + "id": 1, + "position": [ + 1280, + 1100 + ], + "size": [ + 950, + 900 + ], + "type": "frame" + }, + { + "child_steps": [ + 25, + 19, + 20 + ], + "color": "red", + "data": { + "title": "Mashmap paf tracks subworkflow" + }, + "id": 3, + "position": [ + 1280, + 2100 + ], + "size": [ + 960, + 1020 + ], + "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", + "name": "TreeValGalAugTwoHaps", + "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": "For coverage. MUST be fastqsanger. Autodetect uploads return fastq unfortunately although Sanger has been more or less universal for 15 years so manual adjustment may be needed. ", + "content_id": null, + "errors": null, + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "For coverage. MUST be fastqsanger. Autodetect uploads return fastq unfortunately although Sanger has been more or less universal for 15 years so manual adjustment may be needed. ", + "name": "fastqsanger pacbio sequence reads for coverage bigwig track" + } + ], + "label": "fastqsanger pacbio sequence reads for coverage bigwig track", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 40, + "top": 260 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"tag\": null}", + "tool_version": null, + "type": "data_input", + "uuid": "0e1b8776-4c7b-46fa-adbd-5cdb50f24e41", + "when": null, + "workflow_outputs": [] + }, + "1": { + "annotation": "This will be the sequence, divided into individual fasta contigs, on which tracks are arranged and displayed.", + "content_id": null, + "errors": null, + "id": 1, + "input_connections": {}, + "inputs": [ + { + "description": "This will be the sequence, divided into individual fasta contigs, on which tracks are arranged and displayed.", + "name": "Haplotype1 same names" + } + ], + "label": "Haplotype1 same names", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 40, + "top": 400 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"tag\": null}", + "tool_version": null, + "type": "data_input", + "uuid": "42643151-c155-4745-96d5-e39a0eef1937", + "when": null, + "workflow_outputs": [] + }, + "2": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 2, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "hap1name" + } + ], + "label": "hap1name", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 40, + "top": 520 + }, + "tool_id": null, + "tool_state": "{\"default\": \"H1\", \"parameter_type\": \"text\", \"optional\": true}", + "tool_version": null, + "type": "parameter_input", + "uuid": "6eb84f2d-8c87-4676-9b78-f58537360f7e", + "when": null, + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "1c1997b5-044d-48f5-bd97-c36af9a41e09" + } + ] + }, + "3": { + "annotation": "This will be the sequence, divided into individual fasta contigs, on which tracks are arranged and displayed.", + "content_id": null, + "errors": null, + "id": 3, + "input_connections": {}, + "inputs": [ + { + "description": "This will be the sequence, divided into individual fasta contigs, on which tracks are arranged and displayed.", + "name": "Haplotype2 same names" + } + ], + "label": "Haplotype2 same names", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 40, + "top": 620 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"tag\": null}", + "tool_version": null, + "type": "data_input", + "uuid": "078c7cdf-af94-4aaf-ba96-a380d0237972", + "when": null, + "workflow_outputs": [] + }, + "4": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 4, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "hap2name" + } + ], + "label": "hap2name", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 40, + "top": 740 + }, + "tool_id": null, + "tool_state": "{\"default\": \"H2\", \"parameter_type\": \"text\", \"optional\": true}", + "tool_version": null, + "type": "parameter_input", + "uuid": "37d30f59-320f-47ce-a01c-1117278237dc", + "when": null, + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "1b323fb0-1b55-463a-9939-d27f617d090f" + } + ] + }, + "5": { + "annotation": "TTAGGG or CCCTAA for the treeval test data or for vertebrates seems to work. This uses seqtk-telo and seems to give plausible results with the appropriate repeat element for vertebrates....", + "content_id": null, + "errors": null, + "id": 5, + "input_connections": {}, + "inputs": [ + { + "description": "TTAGGG or CCCTAA for the treeval test data or for vertebrates seems to work. This uses seqtk-telo and seems to give plausible results with the appropriate repeat element for vertebrates....", + "name": "telomere repeat to suit species." + } + ], + "label": "telomere repeat to suit species.", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 40, + "top": 820 + }, + "tool_id": null, + "tool_state": "{\"default\": \"CCCTAA\", \"parameter_type\": \"text\", \"optional\": true}", + "tool_version": null, + "type": "parameter_input", + "uuid": "b0b01da5-5496-4add-8a95-df47e5d1e668", + "when": null, + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "5d328a8d-d60f-41c8-8a59-529780dfadf4" + } + ] + }, + "6": { + "annotation": "dfam is problematic. Aves works for birds! That's why there's also a model free one - windowmasker - for comparison.", + "content_id": null, + "errors": null, + "id": 6, + "input_connections": {}, + "inputs": [ + { + "description": "dfam is problematic. Aves works for birds! That's why there's also a model free one - windowmasker - for comparison.", + "name": "dfam taxon for repeatmasker" + } + ], + "label": "dfam taxon for repeatmasker", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 40, + "top": 920 + }, + "tool_id": null, + "tool_state": "{\"default\": \"vertebrates\", \"parameter_type\": \"text\", \"optional\": true}", + "tool_version": null, + "type": "parameter_input", + "uuid": "4457985f-a3a4-46ad-90fb-0696944dfbd7", + "when": null, + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "9956b5ad-ed59-484a-98fd-3706ccfc0355" + } + ] + }, + "7": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 7, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "dfam taxon 2" + } + ], + "label": "dfam taxon 2", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 40, + "top": 1040 + }, + "tool_id": null, + "tool_state": "{\"default\": \"human\", \"parameter_type\": \"text\", \"optional\": true}", + "tool_version": null, + "type": "parameter_input", + "uuid": "f56770bc-f854-40e7-9c84-e2e588367532", + "when": null, + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "0389a54d-365c-4f85-99e5-d2e27072d676" + } + ] + }, + "8": { + "annotation": "The wiggles are all smoothed by measuring over a window with default of 50 bases. 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Unsmoothed, the wiggles are more useful over small distances, but zoomed out, they become clumped so are not shown.", + "content_id": null, + "errors": null, + "id": 2, + "input_connections": {}, + "inputs": [ + { + "description": "The wiggles are all smoothed by measuring over a window with default of 50 bases. 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Not sure if minimap2 mapping preset is right?

.


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