feat: add workflow and assemblies yml files first pass (#206) #207
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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| assemblies: | ||
| - accession: GCF_000002765.6 | ||
| ploidy: haploid | ||
| source: plasmodb.org | ||
| - accession: GCF_000002415.2 | ||
| ploidy: haploid | ||
| ncbi_dataset: true | ||
| - accession: GCA_900093555.2 | ||
| ploidy: haploid | ||
| source: plasmodb.org | ||
| - accession: GCF_900002385.2 | ||
| ploidy: haploid | ||
| source: plasmodb.org | ||
| - accession: GCF_900681995.1 | ||
| ploidy: haploid | ||
| source: plasmodb.org | ||
| - accession: GCF_016801865.2 | ||
| ploidy: diploid | ||
| source: vectorbase.org | ||
| - accession: GCF_015732765.1 | ||
| ploidy: diploid | ||
| source: vectorbase.org | ||
| - accession: GCF_943734735.2 | ||
| ploidy: diploid | ||
| ncbi_dataset: true | ||
| - accession: GCF_000005575.2 | ||
| ploidy: diploid | ||
| source: vectorbase.org | ||
| - accession: GCF_000006565.2 | ||
| ploidy: haploid | ||
| source: toxodb.org | ||
| - accession: GCF_000195955.2 | ||
| ploidy: haploid | ||
| - accession: GCF_018416015.2 | ||
| ploidy: haploid | ||
| ncbi_dataset: true | ||
| - accession: GCA_000170175.2 | ||
| ploidy: haploid | ||
| source: fungidb.org | ||
| - accession: GCF_000149335.2 | ||
| ploidy: haploid | ||
| source: fungidb.org | ||
| - accession: GCF_000209065.1 | ||
| ploidy: diploid | ||
| source: tritrypdb.org | ||
| - accession: GCF_000002445.2 | ||
| ploidy: diploid | ||
| source: tritrypdb.org | ||
| - accession: GCF_000002725.2 | ||
| ploidy: diploid | ||
| source: tritrypdb.org | ||
| - accession: GCF_000227135.1 | ||
| ploidy: diploid | ||
| source: tritrypdb.org | ||
| - accession: GCF_000002845.2 | ||
| ploidy: diploid | ||
| source: tritrypdb.org | ||
| - accession: GCF_009858895.2 | ||
| ploidy: haploid | ||
| - accession: GCF_000857045.1 | ||
| ploidy: haploid | ||
| - accession: GCF_000002655.1 | ||
| ploidy: haploid | ||
| source: fungidb.org | ||
| - accession: GCF_000182965.3 | ||
| ploidy: diploid | ||
| source: fungidb.org | ||
| - accession: GCF_000091045.1 | ||
| ploidy: haploid | ||
| ncbi_dataset: true | ||
| - accession: GCA_000149245.3 | ||
| ploidy: haploid | ||
| source: fungidb.org |
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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." | ||
|
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. |
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| ploidy: "any" | ||
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|
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| - trs_id: "https://dockstore.org/api/ga4gh/trs/v2/tools/#workflow/github.com/iwc-workflows/chipseq-pe/main/versions/v0.12" | ||
| type: "TRANSCRIPTOMICS" | ||
| description: "Analyze bulk or single-cell RNA seq data using a variety of approaches." | ||
| ploidy: "any" | ||
|
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| - trs_id: "https://dockstore.org/api/ga4gh/trs/v2/tools/#workflow/github.com/iwc-workflows/haploid-variant-calling-wgs-pe/main/versions/v0.1" | ||
| type: "VARIANT_CALLING" | ||
| description: "Identify nucleotide polymorphisms and short indels from Illumina and Element data." | ||
| ploidy: "haploid" | ||
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| outbreaks: | ||
| - tax_id: 2697049 | ||
| name: "SARS-CoV-2" | ||
| description: "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the virus responsible for the COVID-19 pandemic." | ||
| - tax_id: 10244 | ||
| name: "Mpoxvirus" | ||
| description: "Monkeypox virus is a member of the Orthopoxvirus genus in the family Poxviridae." |
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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' @mvdbeekThere was a problem hiding this comment.
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oooooooooooo. id vote in favor of versions. very good q.
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the word 'latest' scared me 😨