galaxyproject / galaxyproject/brc-analytics

How to call the "assembly" type workflows?

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#261 3 comments 0 reactions 1 assignee Assigned to @mvdbeek View on GitHub
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Description

We have these assembly workflows identified to be used:

- trs_id: "https://dockstore.org/api/ga4gh/trs/v2/tools/#workflow/github.com/iwc-workflows/assembly-with-flye/main/versions/v0.2"
type: "ASSEMBLY"
description: "Assemble prokaryotic and eukaryotic genomes sequenced with a variety of technologies."
ploidy: "any"

- trs_id: "https://dockstore.org/api/ga4gh/trs/v2/tools/#workflow/github.com/iwc-workflows/bacterial-genome-assembly/main/versions/v1.1.5"
type: "ASSEMBLY"
description: "Assemble prokaryotic and eukaryotic genomes sequenced with a variety of technologies."
ploidy: "any"

To use these workflows do we need to make any updates to [getWorkflowLandingRequestState](https://github.com/galaxyproject/brc-analytics/blob/f3cda2e89b3ddeba5d98a80064e5adfc9d3a0f3d/app/utils/galaxy-api.ts#L73)?

```js
function getWorkflowLandingsRequestState(
workflowId: WORKFLOW_ID,
referenceGenome: string,
geneModelUrl: string | null
): WorkflowLandingsBodyRequestState {
if (workflowId === WORKFLOW_ID.VARIANT_CALLING && geneModelUrl) {
return {
"Annotation GTF": { ext: "gtf.gz", src: "url", url: geneModelUrl },
"Genome fasta": {
ext: "fasta.gz",
src: "url",
url: buildFastaUrl(referenceGenome),
},
};
}
return { reference_genome: referenceGenome };
}

```

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