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    pvanheusden
    @pvanheusden:matrix.org
    [m]
    so... I guess test datasets could be loaded into Data Libraries?
    bwlang (Brad Langhorst) do you have time to contribute to identifying some test datasets for SARS-CoV-2 today? if not, we can start experimenting with some from the US CDC collection...
    I hear talk about Galaxy <-> Observable interoperation... does this perhaps have a role to play (instead of / in addition to the Jupyter notebook)?
    and concretely on comparisons: what tooling is good for comparing VCFs?
    wm75 (Wolfgang Maier)
    @wm75:matrix.org
    [m]
    The observable interoperability could be nice, yes, I'm just not as good in JS as in Python
    pvanheusden
    @pvanheusden:matrix.org
    [m]
    is there a guide to this observable interface somewhere?
    wm75 (Wolfgang Maier)
    @wm75:matrix.org
    [m]
    Stephen Shank: is the most knowledgeable person on this
    Stephen Shank
    @stephenshank:matrix.org
    [m]
    pvanheusden: I'm glad you're interested in Observable. We have a lot of work in progress on this. It's a bit in flux because of development in the co-fest, but I will be sure to follow up next week
    pvanheusden
    @pvanheusden:matrix.org
    [m]
    Sure thing - thanks for the feedback.
    wm75 (Wolfgang Maier)
    @wm75:matrix.org
    [m]
    Copied over from the GCC CoFest slack channel (posted there by Stephen Shank):
    bwlang and I got a quick primer dropout dashboard analysis consuming output from a modified and extended workflow of his. We have a battle plan for a pretty neat tool. https://observablehq.com/@stephenshank/primer-dropout-analysis?payload\_id=4e31fd91f102b951
    pvanheusden
    @pvanheusden:matrix.org
    [m]
    this is great... sorry to be difficult, but once things are prototyped in Observable can they be rendered as HTML? for IRIDA use case I need to render stuff to a (single page) HTML output. it kind of looks do-able because this is vega-lite?
    Stephen Shank
    @stephenshank:matrix.org
    [m]
    Not difficult at all, I am happy to answer any questions to whomever is interested in this platform and/or the integration with Galaxy. Short answer is yes... the notebooks can have trimmed down versions that can be exported as static sites (HTML/JS/CSS) and/or npm packages whose code can be hacked at
    The full runtime is unfortunately not open sourced, so these exports do not allow users to hack/develop once exported. But they have all the UI/interactivity that a developer builds up in the exported version
    Here is an example of how we do this in our own software: https://github.com/veg/hyphy-vision/blob/master/package.json#L26
    pvanheusden
    @pvanheusden:matrix.org
    [m]
    Awesome. And for the amplicon dropout analysis... so something is generating the bedgraph dataset that provides a matrix of mean coverage per amplicon (a Galaxy workflow or tool?). then this is somehow being exported to Observable where vega-lite makes that visualisation. what links the Observable to a Galaxy dataset? Seems to be this: https://observablehq.com/@stephenshank/the-observable-galaxy
    Stephen Shank
    @stephenshank:matrix.org
    [m]
    We ran a few extra steps at the end, included the Observable tool, found in the visualization pane
    Unfortunately it is only on our instance at the moment. We got some nice features done that at the CoFest that will make it more useable. Repo is here, there's an early version on the test toolshed: https://github.com/stephenshank/the\_observable\_galaxy
    Still a WIP
    Stephen Shank
    @stephenshank:matrix.org
    [m]
    This was my attempt to do a minimal reproducible example: https://observablehq.com/@stephenshank/observable-galaxy-mre
    pvanheusden
    @pvanheusden:matrix.org
    [m]
    I see this virological post makes reference to an ESCMID assessment of SARS-CoV-2 assemble / variant detection pipelines: https://virological.org/t/missing-g21987a-mutation-in-sars-cov-2-delta-variants-due-to-non-specific-amplification-by-artic-v3-primers/764/8 - I think it might be this assessment - https://journals.asm.org/doi/10.1128/JCM.01698-21 - frustratingly they don't provide data for the test samples. Also these are all pre-Delta samples
    pvanheusden
    @pvanheusden:matrix.org
    [m]
    nice progress on phylogeny viz / lineage vis tools: https://twitter.com/theosanderson/status/1553070643998081024
    bgruening
    @bgruening:matrix.org
    [m]
    cool!
    there is a docker container already, so should be easy to add as IT I guess
    pvanheusden
    @pvanheusden:matrix.org
    [m]
    wm75 (Wolfgang Maier) experimenting with the new pangolin and the (in PR) new nextclade illustrates the problem I had before with DMs... DM sort order is not configurable, so it, by default, shows the oldest dataset as the default selection.
    wm75 (Wolfgang Maier)
    @wm75:matrix.org
    [m]
    Yeah, we should create a PR to change that. It's an obvious missing feature.
    wm75 (Wolfgang Maier)
    @wm75:matrix.org
    [m]
    Yes, that's the "simple" part. Then we also need to add a new attribute to the tool xml element.
    pvanheusden
    @pvanheusden:matrix.org
    [m]
    in the xsd?
    wm75 (Wolfgang Maier)
    @wm75:matrix.org
    [m]
    btw, I'll look at your nextclade PR later today when I'm out of a workshop that I'm currently giving
    pvanheusden
    @pvanheusden:matrix.org
    [m]
    thanks.
    I guess this is a dev question, but I wonder what the current practice is with Galaxy code and type annotations.
    since Galaxy is now Python 3.8+
    pvanheusden
    @pvanheusden:matrix.org
    [m]
    Stephen Shank just to add another level - Quarto (https://quarto.org/) also has Observable support and makes for a pretty neat notebook-creating tool.
    pvanheusden
    @pvanheusden:matrix.org
    [m]
    wm75 (Wolfgang Maier) I'm trying to understand your SARS-CoV-2 ONT workflow... you run medaka twice, with or without variant realignment and then you accept only those variants that appear in both datasets?
    then you use this merged VCF file to add annotations to the original VCF?
    pvanheusden
    @pvanheusden:matrix.org
    [m]
    what is the annotation you're looking for in these steps?
    pvanheusden
    @pvanheusden:matrix.org
    [m]
    btw I'm testing clair3 vs medaka calls...
    wm75 (Wolfgang Maier)
    @wm75:matrix.org
    [m]
    The answer‘s in the Changelog of the latest iwc version of the WF.
    wm75 (Wolfgang Maier)
    @wm75:matrix.org
    [m]
    The medaka tools annotate script, with default settings, is blind to variants at the very ends of reads. So to get proper INFO fields for primer binding site variants, we need a separate medaka run with adjusted settings.
    That‘s because the Galaxy wrapper runs medaka tools annotate behind the scenes (no separate wrapper).
    It‘s a mess and I‘d switch to clair3 happily, but presumably that will require some similar output massaging too.
    wm75 (Wolfgang Maier)
    @wm75:matrix.org
    [m]
    Since I think clair3 VCFs are lacking some standard INFO keys too.
    pvanheusden
    @pvanheusden:matrix.org
    [m]
    yes clair3 output is not so great. also its output compressed vcf which is not great for all tools. easily fixed with another step but still.
    I'm currently working on a mosdepth wrapper bwlang (Brad Langhorst) I think you might like this - mosdepth has many options for BAM depth reporting
    but will get back to clair3 after that.
    bwlang
    @bwlang:matrix.org
    [m]
    we use mosdepth extensively - great to have a wrapper for it!
    pvanheusden
    @pvanheusden:matrix.org
    [m]
    bwlang (Brad Langhorst) PR in progress here - galaxyproject/tools-iuc#4751 - I had persist errors getting replicable results so tests fail but feel free to have a look / dive in