feat: add workflow and assemblies yml files first pass (#206) #207
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| workflows: | ||
| - trs_id: "https://dockstore.org/api/ga4gh/trs/v2/tools/#workflow/github.com/iwc-workflows/rnaseq-pe/main/versions/v0.9" | ||
| type: "REGULATION" | ||
| description: "Workflows for the analysis of ChIP-seq, ATAC-Seq, and beyond." |
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are these descriptions for the workflows? or for the 'type' ?
there will eventually be many workflows belonging to a 'type' (or whatever we end up calling it.. type is too vague imo), and i wonder if this source of duplication implies a need for a new yaml file?
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Yes, reading the descriptions, I agree they should like they describe the workflow type rather than a specific workflow within the type. I think this came from having only one workflow per type for the initial kickoff. Sounds like we do need a type (or "modality?) tab.
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I think we could also add (or generate) links to view the workflow details in GitHub, Dockstore etc. or wherever they live.
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Can/should we align these 'types' with the collection as organized on dockstore (and iwc site)? (https://dockstore.org/organizations/iwc)
This can be programmatically fetched if so.
files/source/galaxy_workflows.yml
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| workflows: | |||
| - trs_id: "https://dockstore.org/api/ga4gh/trs/v2/tools/#workflow/github.com/iwc-workflows/rnaseq-pe/main/versions/v0.9" | |||
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I think the actual trsID here is just #workflow/github.com/iwc-workflows/rnaseq-pe/main, though it does bring up how we want to pin specific versions (or not). Do we want an explicit extra step to update this annotation as new versions are released, or do we want 'latest' @mvdbeek
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oooooooooooo. id vote in favor of versions. very good q.
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the word 'latest' scared me 😨
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I think the actual trsID here is just
#workflow/github.com/iwc-workflows/rnaseq-pe/main, though it does bring up how we want to pin specific versions (or not)
No, this is the full TRS id as we need it. No, no latest, we should always use pinned versions.
files/source/galaxy_workflows.yml
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| - trs_id: "#workflow/github.com/iwc-workflows/generic-variant-calling-wgs-pe/main" | ||
| type: "VARIANT_CALLING" | ||
| description: "Identify nucleotide polymorphisms and short indels from Illumina and Element data." | ||
| ploidy: "any" |
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I think this is meant for haploid / non-diploid organisms. @nekrut I think you wrote this one ?
files/source/galaxy_workflows.yml
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| description: "Best practices for assembly of prokaryotic and eukaryotic genomes sequenced with a variety of technologies." | ||
| ploidy: "any" | ||
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| # idk yet what makes this specific to bacteria, or if it can be easily generalized |
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Thanks. maybe it's enough to annotate as haploid then..
files/source/galaxy_workflows.yml
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| - trs_id: "#workflow/github.com/iwc-workflows/assembly-with-flye/main" | ||
| type: "ASSEMBLY" | ||
| description: "Best practices for assembly of prokaryotic and eukaryotic genomes sequenced with a variety of technologies." |
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The description is repeated, but also weird ? Maybe stick to the Workflow for ... pattern you've used above.
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Yea I think these could use work. For now I was just replicating what was on the site as category descriptions.
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Ok then, we have incorporated the assemblies.yml on to main. I am will close this PR and the related ticket and reopen two new tickets, one for workflows and one for the outbreak information. |
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@NoopDog ive just about got ready the assemblies yaml w the 778 we had before, now annotated and in the right format etc. let me know where to put that and when.. |
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@d-callan, you can PR your new assemblies in https://github.com/galaxyproject/brc-analytics/blob/main/catalog-build/source/assemblies.yml in a new PR against main. |
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idk when exactly we need them, just remembered hearing on the call w wiriya it sounded like we wanted them back soon. i dont mind holding on to it a bit longer, or making a draft PR and letting it sit there if others would like a look. |
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Cool, I will set you up for the draft PR in a bit. @d-callan Thx! |
Added files for Assembly (Input) and Workflows matching this evolving schema doc.