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?
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 ?
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-19Applying 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 😆
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
the schema is used to validate the workflow, but gxformat2 contains functions for the conversion that don't depend on the schema
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
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.
yes that's kind of what I meant... so where is the schema actually used?
aha, so it should co-evolve with the code for linting purposes... nod
Carole just proposed we should be renaming to "Intergalactic Workflow Constellation" :)
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 😛
Yeah, but I think we fixed that in a more recent galaxy-tool-util release ?!
Is that still failing in CI ?
this one's newer and doesn't specify attributes: https://github.com/galaxyproject/iwc/blob/1d69747e43ec0db6bc09c87a9e70389482b52690/workflows/data-fetching/parallel-accession-download/parallel-accession-download-tests.yml
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>}]
yes
there's a bunch of different possible causes, like filtered out outputs or bugs
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
I can also try and create a more minimal case
it seems it isn't possible to add citations to a workflow, as it is for tools?
would be a useful feature imo
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