feat: add workflow and assemblies yml files first pass (#206) #207
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| assemblies: | ||
| # plasmodium falciparum | ||
| - accession: GCF_000002765.6 | ||
| ploidy: haploid | ||
| source: plasmodb.org | ||
| # plasmodium vivax | ||
| - accession: GCF_000002415.2 | ||
| ploidy: haploid | ||
| ncbi_dataset: true | ||
| - accession: GCA_900093555.2 | ||
| ploidy: haploid | ||
| source: plasmodb.org | ||
| # plasmodium yoelii | ||
| - accession: GCF_900002385.2 | ||
| ploidy: haploid | ||
| source: plasmodb.org | ||
| # plasmodium vinckei | ||
| - accession: GCF_900681995.1 | ||
| ploidy: haploid | ||
| source: plasmodb.org | ||
| # culex p. pallens | ||
| - accession: GCF_016801865.2 | ||
| ploidy: diploid | ||
| source: vectorbase.org | ||
| # culex p. quinquefasciatus | ||
| - accession: GCF_015732765.1 | ||
| ploidy: diploid | ||
| source: vectorbase.org | ||
| # anopheles gambiae | ||
| - accession: GCF_943734735.2 | ||
| ploidy: diploid | ||
| ncbi_dataset: true | ||
| - accession: GCF_000005575.2 | ||
| ploidy: diploid | ||
| source: vectorbase.org | ||
| # toxoplasma gondii | ||
| - accession: GCF_000006565.2 | ||
| ploidy: haploid | ||
| source: toxodb.org | ||
| # mycobacterium tuberculosis | ||
| - accession: GCF_000195955.2 | ||
| ploidy: haploid | ||
| # coccidioides posadasii | ||
| - accession: GCF_018416015.2 | ||
| ploidy: haploid | ||
| ncbi_dataset: true | ||
| - accession: GCA_000170175.2 | ||
| ploidy: haploid | ||
| source: fungidb.org | ||
| # coccidioides immitis | ||
| - accession: GCF_000149335.2 | ||
| ploidy: haploid | ||
| source: fungidb.org | ||
| # trypanosoma cruzi | ||
| - accession: GCF_000209065.1 | ||
| ploidy: diploid | ||
| source: tritrypdb.org | ||
| # trypanosoma brucei | ||
| - accession: GCF_000002445.2 | ||
| ploidy: diploid | ||
| source: tritrypdb.org | ||
| # leishmania major | ||
| - accession: GCF_000002725.2 | ||
| ploidy: diploid | ||
| source: tritrypdb.org | ||
| # leishmania donovani | ||
| - accession: GCF_000227135.1 | ||
| ploidy: diploid | ||
| source: tritrypdb.org | ||
| # leishmania braziliensis | ||
| # danielle's favorite | ||
| - accession: GCF_000002845.2 | ||
| ploidy: diploid | ||
| source: tritrypdb.org | ||
| # covid | ||
| - accession: GCF_009858895.2 | ||
| ploidy: haploid | ||
| # mpox | ||
| - accession: GCF_000857045.1 | ||
| ploidy: haploid | ||
| # aspergillus fumigatus | ||
| - accession: GCF_000002655.1 | ||
| ploidy: haploid | ||
| source: fungidb.org | ||
| # candida albicans | ||
| - accession: GCF_000182965.3 | ||
| ploidy: diploid | ||
| source: fungidb.org | ||
| # crypococcus neoformans | ||
| - accession: GCF_000091045.1 | ||
| ploidy: haploid | ||
| ncbi_dataset: true | ||
| - accession: GCA_000149245.3 | ||
| ploidy: haploid | ||
| source: fungidb.org |
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| workflows: | ||
| # this list of workflows and their annotations are a wip and will be updated as i learn more | ||
| # about their status and the tools used, etc. | ||
| - trs_id: "#workflow/github.com/iwc-workflows/chipseq-pe/main" | ||
| type: "REGULATION" | ||
| description: "Workflows for the analysis of ChIP-seq, ATAC-Seq, and beyond." | ||
| ploidy: "any" | ||
|
|
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| - trs_id: "#workflow/github.com/iwc-workflows/chipseq-sr/main" | ||
| type: "REGULATION" | ||
| description: "Workflows for the analysis of ChIP-seq, ATAC-Seq, and beyond." | ||
| ploidy: "any" | ||
|
|
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| - trs_id: "#workflow/github.com/iwc-workflows/rnaseq-pe/main" | ||
| type: "TRANSCRIPTOMICS" | ||
| description: "Analyze bulk or single-cell RNA seq data using a variety of approaches." | ||
| ploidy: "any" | ||
|
|
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| - trs_id: "#workflow/github.com/iwc-workflows/rnaseq-sr/main" | ||
| type: "TRANSCRIPTOMICS" | ||
| description: "Analyze bulk or single-cell RNA seq data using a variety of approaches." | ||
| ploidy: "any" | ||
|
|
||
| - trs_id: "#workflow/github.com/iwc-workflows/haploid-variant-calling-wgs-pe/main" | ||
| type: "VARIANT_CALLING" | ||
| description: "Identify nucleotide polymorphisms and short indels from Illumina and Element data." | ||
| ploidy: "haploid" | ||
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| # im starting to wonder looking at this if the default for ploidy shouldnt be any | ||
| # maybe it could be multivalued [haploid, diploid].. might not matter depending on ui | ||
| - 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 ? |
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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." | ||
|
There was a problem hiding this comment. The description is repeated, but also weird ? Maybe stick to the There was a problem hiding this comment. 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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| 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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There was a problem hiding this comment. There was a problem hiding this comment. Thanks. maybe it's enough to annotate as haploid then.. |
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| # but we may need a new annotation once i figure it out | ||
| - trs_id: "#workflow/github.com/iwc-workflows/bacterial-genome-assembly/main" | ||
| type: "ASSEMBLY" | ||
| description: "Best practices for assembly of prokaryotic and eukaryotic genomes sequenced with a variety of technologies." | ||
| ploidy: "any" | ||
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| outbreaks: | ||
| - outbreak: | ||
| tax_id: 2697049 | ||
| resources: | ||
| - resource: | ||
| title: "Coronavirus: Update Related to the Current Outbreak of COVID-19" | ||
| url: "https://pmc.ncbi.nlm.nih.gov/articles/PMC7139198/" | ||
| - resource: | ||
| title: "COVID-19 Pandemic: A Review of the Global Response" | ||
| url: "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7162758/" | ||
| - resource: | ||
| title: "The Impact of COVID-19 on Public Health" | ||
| url: "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7275854/" | ||
| - resource: | ||
| title: "COVID-19: Epidemiology, Virology, and Clinical Features" | ||
| url: "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7159299/" | ||
| - outbreak: | ||
| tax_id: 10244 | ||
| resources: | ||
| - resource: | ||
| title: "Mpox Virus: Understanding the Outbreak" | ||
| url: "https://example.com/mpox-outbreak" | ||
| - resource: | ||
| title: "Mpox Virus: Symptoms and Treatment" | ||
| url: "https://example.com/mpox-symptoms-treatment" | ||
| - resource: | ||
| title: "Global Response to the Mpox Outbreak" | ||
| url: "https://example.com/global-response-mpox" |
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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.