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Add searchable table for organism-specific parameters in TheiaCoV doc…
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…umentation
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Michal-Babins committed Dec 4, 2024
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Expand Up @@ -477,6 +477,8 @@ All TheiaCoV Workflows (not TheiaCoV_FASTA_Batch)

The `organism_parameters` sub-workflow is the first step in all TheiaCoV workflows. This step automatically sets the different parameters needed for each downstream tool to the appropriate value for the user-designated organism (by default, `"sars-cov-2"` is the default organism).

<div class="searchable-table" markdown="1">

!!! dna ""
The following tables include the relevant organism-specific parameters; **all of these default values can be overwritten by providing a value for the "Overwrite Variable Name" field**.

Expand Down Expand Up @@ -594,6 +596,7 @@ The `organism_parameters` sub-workflow is the first step in all TheiaCoV workflo
| primer_bed_file | HIV-v2 | gs://theiagen-public-files/terra/hivgc-files/HIV-1_v2.0.primer.hyphen400.1.bed | This version of HIV originates from Southern Africa |
| reference_genome | HIV-v2 | gs://theiagen-public-files/terra/hivgc-files/AY228557.1.headerchanged.fasta | This version of HIV originates from Southern Africa |
| reference_gff_file | HIV-v2 | gs://theiagen-public-files/terra/hivgc-files/AY228557.1.gff3 | This version of HIV originates from Southern Africa |
</div>

### Workflow Tasks

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