Long vgp tutorial edits #4542
Long vgp tutorial edits #4542
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@nekrut let me know when this is ready for review :) |
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I think he forgot over the holidays. |
it seems unused, and it we have customizable FAQs for uploading already
shiltemann
requested review from
a team,
bebatut,
hexylena and
shiltemann
as code owners
No - no, just busy with something else. Will resume soon... |
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@nekrut I made some minor tweaks on the technical/framework side, and added some border for figures (currently only for figures with captions)
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would be great to keep a copy of the workflow in the GTN (also for testing purposes)
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yes. But let them stabilize a little.They are tested via IWC mechanics. It is in fact quire difficult to test assembly workflows because underlying test data is usually large. Let's keep them outside for now.
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We just need a workflow here that reflects the steps that are in the tutorial, as a resource for learners and instructors. If the tutorial corresponds exactly to the IWC workflow, just add a copy here. If not, please generate a workflow that matches the tutorial. If tests are problematic we will accept it without.
I can help if needed.
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Can you guarantee that users will get the workflow via TRS and not through the potentially out of date and not automatically updatable workflow in the GTN ?
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The GTN workflow only needs to be up-to-date with the hands-on steps as written in the tutorial, not the latest version of the VGP workflow in general. In the tutorial text you can still point to the WFH/IWC as the main source for the latest version.
(Maybe I misunderstood what you mean?)
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fwiw, in this version of the tutorial learners are not instructed to use a WF at all, only perform all the steps manually.
Ready |
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| ## Genome profiling with **GenomeScope2** |
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you don't need this div, you can just link to #genome-profiling-with-genomescope2 (found via clicking on the link from the agenda on the published page)
| We have obtained the fully phased contig graphs (as {GFA} files) of hap1 and hap2, but these must be converted to FASTA format for subsequent steps. We will use a tool developed from the VGP: **gfastats**. gfastats is a tool suite that allows for manipulation and evaluation of FASTA and GFA files, but in this instance we will use it to convert our GFAs to FASTA files. Later on we will use it to generate standard summary statistics for our assemblies. | ||
| We have obtained the fully phased contig graphs (as {GFA} files) of hap1 and hap2, but these must be converted to FASTA format for subsequent steps. We will use a tool developed from the VGP: [`gfastats`](https://github.com/vgl-hub/gfastats). `gfastats` is a tool suite that allows for manipulation and evaluation of FASTA and GFA files, but in this instance we will use it to convert our GFAs to FASTA files. Later on we will use it to generate standard summary statistics for our assemblies. | ||
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| <div id="hap1_contigs"> |
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all hands on boxes can be linked to, see them on the page, they have a "link to here" button. https://training.galaxyproject.org/training-material/topics/assembly/tutorials/vgp_genome_assembly/tutorial.html#hands-on-convert-gfa-to-fasta
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One problem with anchors is that if the tutorial uses branching (cyoa) and the anchor within a branch that is not selected at the moment - it does not work. Also, there may be hands-on boxes with identical names and these seem to be resolved with numbers that keep incrementing. Anyway - I did remove these.
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Paper is on its way! Thanks, everyone! |
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