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    pvanheusden
    @pvanheusden:matrix.org
    [m]
    so getting back to the gxformat2 - with the current limitations - author, license, etc - it doesn't make sense to have planemo auto-convert? and what is the extension for a gxformat2 file? .yaml or .gxformat2?
    Marius
    @mvdbeek:matrix.org
    [m]
    .yaml
    pvanheusden
    @pvanheusden:matrix.org
    [m]
    ok.... and the issue with missing bits is that they're not in the schema-salad spec here: https://github.com/galaxyproject/gxformat2/blob/master/schema/v19_09/workflow.yml ?
    Marius
    @mvdbeek:matrix.org
    [m]
    actually, forget what I said
    yes, it's not in the schema, but it only doesn't lint correctly
    it is all in the gxformat2
    class: GalaxyWorkflow
    doc: Find and annotate variants in SARS-CoV-2 samples sequenced with Illumina ARTICv3
    label: SARS-CoV-2 Illumina Amplicon pipeline - iVar based
    creator:
    - class: Person
      identifier: 0000-0001-6553-5274
      name: Peter van Heusden
    license: MIT
    release: '0.2'
    tags:
    - COVID-19
    Applying linter structure... FAIL
    .. ERROR: Validation failed - tried _RecordLoader but
      Trying 'GalaxyWorkflow'
    pe-wgs-ivar-analysis.ga.gxwf.yml:4:1:     invalid field `creator`, expected one of: `id`, `label`,
                                              `doc`, `inputs`, `outputs`, `uuid`, `class`, `steps`,
                                              `report`, `tags`
    - tried _ArrayLoader but
      Expected a list
    Applying linter tests... WARNING
    .. WARNING: Workflow missing test cases.
    I worked on it a little while ago, and gave up frustrated when everything was working fine but was then garbled up when deployed to dockstore 😆
    Nicola Soranzo
    @nsoranzo:matrix.org
    [m]
    pvanheusden
    @pvanheusden:matrix.org
    [m]
    ok I think I should be careful falling into this rabbit hole. what do you mean "is in gxformat2" but not in the schema? I thought the schema was the format
    Nicola Soranzo
    @nsoranzo:matrix.org
    [m]
    I guess Galaxy adds extra fields not yet in the schema?
    Marius
    @mvdbeek:matrix.org
    [m]
    the schema is used to validate the workflow, but gxformat2 contains functions for the conversion that don't depend on the schema
    John Chilton
    @jmchilton:matrix.org
    [m]
    the schema is an attempt to model the format - I wouldn't describe it as the format :|
    Unlike CWL say where it is pretty explicitly the format. I'm just not good enough at JSON LD or schema salad to make that perfect. Maybe someday
    pvanheusden
    @pvanheusden:matrix.org
    [m]
    ok so the "format" is the Python code?
    John Chilton
    @jmchilton:matrix.org
    [m]
    that question is a bit too philosophical for me 😅, if I was forced to give a definition of the format I'd make it an empirical one based on what Galaxy runs.
    pvanheusden
    @pvanheusden:matrix.org
    [m]
    yes that's kind of what I meant... so where is the schema actually used?
    John Chilton
    @jmchilton:matrix.org
    [m]
    linting, documentation, code generation for Java models
    pvanheusden
    @pvanheusden:matrix.org
    [m]
    aha, so it should co-evolve with the code for linting purposes... nod
    John Chilton
    @jmchilton:matrix.org
    [m]
    yes
    Marius
    @mvdbeek:matrix.org
    [m]
    We've got the montly WG call in 10 minutes: meet.google.com/myu-vozy-bsj
    wm75 (Wolfgang Maier)
    @wm75:matrix.org
    [m]
    Shoot, didn't realize. I joined another meeting.
    bgruening
    @bgruening:matrix.org
    [m]
    Carole just proposed we should be renaming to "Intergalactic Workflow Constellation" :)
    Simon Bray
    @simonbray:matrix.org
    [m]
    Question: does the attributes: {} in IWC tests for collection outputs have any purpose?
    Apart from causing tests to fail if it's not included, I mean 😛
    Marius
    @mvdbeek:matrix.org
    [m]
    Yeah, but I think we fixed that in a more recent galaxy-tool-util release ?!
    Is that still failing in CI ?
    Simon Bray
    @simonbray
    Ah, good to know, I am testing locally. I'll try updating galaxy-tool-util
    Simon Bray
    @simonbray:matrix.org
    [m]
    Hello, I'm currently encountering the following Planemo error for the last step of my workflow:
    Traceback (most recent call last):
      File "/home/simon/GitRepos/planemo/planemo/galaxy/activity.py", line 50, in execute
        return _execute(ctx, config, runnable, job_path, **kwds)
      File "/home/simon/GitRepos/planemo/planemo/galaxy/activity.py", line 219, in _execute
        run_response.collect_outputs(ctx, output_directory)
      File "/home/simon/GitRepos/planemo/planemo/galaxy/activity.py", line 366, in collect_outputs
        output_src = self.output_src(runnable_output)
      File "/home/simon/GitRepos/planemo/planemo/galaxy/activity.py", line 567, in output_src
        raise Exception("Failed to find output [%s] in invocation outputs [%s]" % (output_name, invocation["outputs"]))
    There is a corresponding message in the Galaxy logs: galaxy.workflow.run DEBUG 2021-10-27 17:46:24,479 [pN:main.web.1,p:11036,w:1,m:0,tN:WorkflowRequestMonitor.monitor_thread] Failed to find expected workflow output [outp_col] in step outputs [{'outp': <galaxy.model.HistoryDatasetAssociation(2228) at 0x7f4a0e35a668>, 'outp_frict': <galaxy.model.HistoryDatasetAssociation(2229) at 0x7f4a0e35aa20>}]
    Marius
    @mvdbeek:matrix.org
    [m]
    ah, nice, a reproducible case!
    Simon Bray
    @simonbray:matrix.org
    [m]
    Wondering if anyone has seen something similar to that before?
    Marius
    @mvdbeek:matrix.org
    [m]
    can you share this, we need to improve the error reporting
    yes
    there's a bunch of different possible causes, like filtered out outputs or bugs
    Simon Bray
    @simonbray:matrix.org
    [m]
    fwiw, maybe it's related, but whenever I open the workflow in the editor, it always tries to delete the final connection (to the problematic output) if I try and modify the tool
    anyway, I was planning to make an IWC PR, so I will push it there
    Marius
    @mvdbeek:matrix.org
    [m]
    yeah, that could well be possible
    Simon Bray
    @simonbray:matrix.org
    [m]
    Marius galaxyproject/iwc#68 if you want to have a look
    I can also try and create a more minimal case
    Marius
    @mvdbeek:matrix.org
    [m]
    that would be awesome
    Simon Bray
    @simonbray:matrix.org
    [m]
    it seems it isn't possible to add citations to a workflow, as it is for tools?
    would be a useful feature imo
    Marius
    @mvdbeek:matrix.org
    [m]
    I agree, can you open an issue for this on the galaxy repo ?
    Marius
    @mvdbeek:matrix.org
    [m]
    I'm prepping to look into the minimal workflow you posted Simon Bray , one thing I noticed is that gmx_sim isn't at the latest version. Might be totally unrelated of course