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Repo info
Activity
    Marius
    @mvdbeek:matrix.org
    [m]
    Note that only works for selects, not conditionals, since conditionals can add arbitrary inputs and outputs, breaking workflows
    pvanheusden
    @pvanheusden:matrix.org
    [m]
    "add connection to module" button is the <-> ?
    Marius
    @mvdbeek:matrix.org
    [m]
    yes
    pvanheusden
    @pvanheusden:matrix.org
    [m]
    ah damn, the staramr input is a conditional - instead of making it "use pointfinder: yes / no" and then "which database", they (PHAC-NML) combined it into one
    Marius
    @mvdbeek:matrix.org
    [m]
    I think this particular conditional could be flattened by moving the unvalidated one into the main select, then checking whether or not the custom flag is needed in cheetah
    Marius
    @mvdbeek:matrix.org
    [m]
    The next workflows call is in 60 minutes:
    Workflow WG call
    Thursday, 17 November ยท 16:00 โ€“ 17:00
    Google Meet joining info
    Video call link: https://meet.google.com/myu-vozy-bsj
    Lucille Delisle
    @lldelisle
    I won't be able to join because I have another seminar at the same time but please keep me updated if you find an agreement on the multiple workflow directory.
    Marius
    @mvdbeek:matrix.org
    [m]
    Sounds like there's some movement on the workflowhub side, but will do!
    Marius
    @mvdbeek:matrix.org
    [m]
    wm75 (Wolfgang Maier)
    @wm75:matrix.org
    [m]
    Sorry, trapped in a grant meeting the whole afternoon.
    Marius
    @mvdbeek:matrix.org
    [m]
    I think I got most of the backend modalities worked out for conditional steps, if you want to have a look at the test case and assumptions, they're in lib/galaxy_test/api/test_workflows.py here: https://github.com/galaxyproject/galaxy/pull/14846/files#diff-62218e13fbfad227cca222eb36d1801285ceb01eb2f9eb0c14aa99175bddd762R1896 ... no UI yet, that's the next thing I'll work on
    Lucille Delisle
    @lldelisle
    This looks super great!
    Thanks
    Just for information, this could be part of 23.0? Is that the idea?
    Marius
    @mvdbeek:matrix.org
    [m]
    Yes, I hope so!
    Guess we got ~ 2-3 weeks to get the user interface in, it seems doable if there's no too many unexpected things popping up
    Lucille Delisle
    @lldelisle
    Some iuc tools are not up to date in usegalaxy.org, this makes some upgrade PR failing, would it be possible to update them (toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1 and toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.0+galaxy0).
    Thanks
    Marius
    @mvdbeek:matrix.org
    [m]
    I tried this morning, but we have to wait for the bioconductor rebuild to finish
    otherwise we may not have all dependencies on usegalaxy.org
    Lucille Delisle
    @lldelisle
    ok no problem, I did not know you were aware
    Delphine Lariviere
    @delphine-l:matrix.org
    [m]
    what is the rule for subworkflows in the iwc repo? should i have a separate folder with tests or is it enought that they are tested in the main workflows ?
    Marius
    @mvdbeek:matrix.org
    [m]
    If they're useful on their own it certainly is easier for you to have separate tests, yeah
    Delphine Lariviere
    @delphine-l:matrix.org
    [m]
    ok
    M Bernt
    @bernt-matthias:matrix.org
    [m]
    What can/should be done about tool versions used in a workflow that are missing on usegalaxy.org? If someone tells me I would add it here: https://github.com/galaxyproject/iwc/blob/main/workflows/README.md#optional-updating-tools :)
    (its the newest version of the NCBI dataset download tool)
    Marius
    @mvdbeek:matrix.org
    [m]
    that's here: https://github.com/galaxyproject/usegalaxy-tools#requesting-a-new-tool-or-updating-a-tool ... but don't add it, we'll automate this, that's just extra cognitive load
    (also we should be able to install tools as well during tests)
    Lucille Delisle
    @lldelisle
    (When we set up the readme we did not dare putting 'ask Marius if a tool is missing') ;-)
    Marius
    @mvdbeek:matrix.org
    [m]
    Delphine Lariviere
    @delphine-l:matrix.org
    [m]
    Marius
    @mvdbeek:matrix.org
    [m]
    and the minute we hung up it passed ๐Ÿ˜†
    Delphine Lariviere
    @delphine-l:matrix.org
    [m]
    of course \o/
    awesome
    Marius
    @mvdbeek:matrix.org
    [m]
    Delphine Lariviere
    @delphine-l:matrix.org
    [m]
    haha nice ugly plot
    Marius
    @mvdbeek:matrix.org
    [m]
    believable though, given the other plots ;)
    Delphine Lariviere
    @delphine-l:matrix.org
    [m]
    that would have been a strange error to have otherwise
    Marius
    @mvdbeek:matrix.org
    [m]
    1 reply
    Jennifer Hillman-Jackson
    @jennaj:matrix.org
    [m]
    Hi all -- is this even possible? Guessing the workflow invocation view needs to access the server's existing HTML "allow-list". https://help.galaxyproject.org/t/how-to-display-multiqc-report-in-workflow-invocation-report/9115
    Jennifer Hillman-Jackson
    @jennaj:matrix.org
    [m]
    I'm testing this out at ORG in a fresh history. Maybe they are working at a local server and just need to add the tool to their allowlist
    Nicola Soranzo
    @nsoranzo:matrix.org
    [m]
    Probably
    Jennifer Hillman-Jackson
    @jennaj:matrix.org
    [m]
    I had misunderstood what they wanted (maybe). From "User > Workflow invocations" the outputs are listed out and drilling down to HTML output is rendered correctly. BUT I think what they want is to add in are output datasets to the "Report" function. No other outputs are fully rendered -- the report just has the workflow/tool parameters, and I think that is fine. I'll write them back with the how-to for all cases.
    Delphine Lariviere
    @delphine-l:matrix.org
    [m]
    thanks a lot !
    Lucille Delisle
    @lldelisle
    Hi there,
    All green except 1:
    image.png
    I guess it is an issue with the delta which is too low.
    Marius
    @mvdbeek:matrix.org
    [m]
    I guess it would be helpful to know what the delta that we get in the test actually is ๐Ÿค”
    M Bernt
    @bernt-matthias:matrix.org
    [m]
    I'm using this cut tool in a workflow (on 22.01) .. the workflow has then always extra chars in the field selector, i.e. the command line is cut -f '1__cn__'... which fails. Is there a trick to this?
    Marius
    @mvdbeek:matrix.org
    [m]
    update galaxy, then Galaxy strips the newline that the editor adds