feat: add workflow and assemblies yml files first pass (#206) #207
Conversation
| 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." |
There was a problem hiding this comment.
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?
There was a problem hiding this comment.
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.
There was a problem hiding this comment.
I think we could also add (or generate) links to view the workflow details in GitHub, Dockstore etc. or wherever they live.
There was a problem hiding this comment.
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
Outdated
| @@ -0,0 +1,15 @@ | |||
| workflows: | |||
| - trs_id: "https://dockstore.org/api/ga4gh/trs/v2/tools/#workflow/github.com/iwc-workflows/rnaseq-pe/main/versions/v0.9" | |||
There was a problem hiding this comment.
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
There was a problem hiding this comment.
oooooooooooo. id vote in favor of versions. very good q.
There was a problem hiding this comment.
the word 'latest' scared me 😨
| - 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" |
There was a problem hiding this comment.
I think this is meant for haploid / non-diploid organisms. @nekrut I think you wrote this one ?
| description: "Best practices for assembly of prokaryotic and eukaryotic genomes sequenced with a variety of technologies." | ||
| ploidy: "any" | ||
|
|
||
| # idk yet what makes this specific to bacteria, or if it can be easily generalized |
There was a problem hiding this comment.
|
|
||
| - 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." |
There was a problem hiding this comment.
The description is repeated, but also weird ? Maybe stick to the Workflow for ... pattern you've used above.
Added files for Assembly (Input) and Workflows matching this evolving schema doc.