Create readme for workfow usage

workflows/VGP-assembly-v2/Curation-TreeValGal/README.md

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+# TreeValGal workflow
+
+Workflow to generate pre-curation files and Jbrowse2 instance.
+
+## Inputs 
+
+### Mandatory
+
+- `Genome assembly to report on` Single halotypes or concatenated haplotypes (If concatenating the haplotypes, windowmasker could fail. In that case, try re-runing with the option `Run windowmasker model-free repeats?` set as `No`)
+- `fastqsanger pacbio sequence reads for coverage bigwig track` Concatenated PacBio reads
+
+### Optional
+
+- `Window size for bed to bigwig` Set the window size to generate the histogram tracks (coverage, gaps...)
+- `dfam taxon for repeatmasker` Default is vertebrates. A more accurate taxon means more accurate repeat recognition 
+- `telomere repeat to suit species` Default : CCCTAA. Seems to work for the treeval test data or for vertebrates . 
+
+#### Annotations
+
+You have the option to provide fasta files for different features. they will be aligned against the assembly and shown in Jbrowse2. 
+
+CDS:
+- Set `Will you provide a CDS fasta for annotation?` as `yes` and provide a Fasta in `CDS fasta input`
+
+Genes
+- Set `Will you provide a genes fasta for annotation?` as `yes` and provide a Fasta in `genes fasta input`
+
+RNA
+- Set `Will you provide a rna fasta for annotation?` as `yes` and provide a Fasta in `rna fasta input`
+
+Proteins
+- Set `Will you provide a protein (AA) fasta for annotation?` as `yes` and provide a Fasta in `AA fasta input`
+
+
+#### Sequence similarity Mapping
+
+You have the option to provide fasta files for a reference or a closely related species (Can also be used to provide the other haplotype of your asembly). These files will be used to produce synteny dotplots and displayed in Jbrowse. 
+
+Independent Reference Genome. The dotplot produced will be filtered with a higher sequence identity: 97%, 98%, and 99%. Suitable for same species genome. 
+- Set `Will you supply an independent reference genome fasta for sequence similarity "self comparison" mapping? This generates paf tracks viewable as contig dotplots.` to `yes` and provide a fasta of the genome in `Independent haplotype or reference genome if available`
+
+Closely related species. The dotplot produced will be filtered with a lower sequence identity: 85%, 93%, and 95%. Suitable for same species genome. 
+- Set `Will you provide a collection of related species for sequence similarity mapping?` to `yes` and provide a **collection** of fasta of one or more related genomes in `Collection of related species`
+
+
+## Outputs
+
+- A Jbrowse2 instance (on for viewing, in `html` the other for export or download in `zip`)
+- Files corresponding to the tracks in Jbrowse2
+
+
+## Display tracks in Jbrowse2
+
+- Add a track:  click on the menu icon (`1` in the Jbrowse2 screenshot below) and click on `Open Track Selector`. Select or deselect the desired tracks
+- Add dotplote: clid `Add` on the top bar and select `Dotplot View`. Then chose the species to display and click `Launch` (several dotplots can be displayed that way). To display a different identity threshold between the to selected species. Click on the menu icon in the Dotplot Window (`2` in the Jbrowse2 screenshot below) and click on `Open Track Selector`. Select the desired Identity threshold.(Warning, selecting more than one track here will overlay the dotplots) 
+
+![Screenshot of Jbrowse2 Instance](img/Jbrowse2.png)