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Testing Docs fix for diagrams on tablet
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Graeme Ford committed Nov 29, 2023
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127 changes: 80 additions & 47 deletions docs/02-workflow/02-methodology-summary.md
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Expand Up @@ -148,7 +148,7 @@ A breakdown of the methodology and softwares used in this workflow.

```mermaid
flowchart TD
wipeInfo[[wipeInfo:\nRemove INFO column for\ncomputational processing\n efficiency]]
wipeInfo[[wipeInfo:\nRemove INFO column for\ncomputational processing\n efficiency]]
```

<dl>
Expand Down Expand Up @@ -176,10 +176,10 @@ A breakdown of the methodology and softwares used in this workflow.
<code>normalize</code>
</summary>

```mermaid
flowchart TD
normalize[[normalize:\nNormalize all SNPs]]
```
```mermaid
flowchart TD
normalize[[normalize:\nNormalize all SNPs]]
```

<dl>
<dt>Function</dt>
Expand Down Expand Up @@ -216,7 +216,7 @@ normalize[[normalize:\nNormalize all SNPs]]

```mermaid
flowchart TD
sort[[sort:\nEnsure correct variant order]]
sort[[sort:\nEnsure correct variant order]]
```

This rule is responsible for sorting variants according to position, relative to the provided reference genome. This is important for downstream analysis which assumes ordered variants.
Expand Down Expand Up @@ -252,7 +252,7 @@ normalize[[normalize:\nNormalize all SNPs]]

```mermaid
flowchart TD
filter[[filter:\nRemove all variant types\nexcept SNPs]]
filter[[filter:\nRemove all variant types\nexcept SNPs]]
```

<dl>
Expand Down Expand Up @@ -286,7 +286,7 @@ normalize[[normalize:\nNormalize all SNPs]]

```mermaid
flowchart TD
annotate[[annotate:\nAnnotate VCF against given\nreference VCF such as \n dbSNP, and rename any unknown\nvariants.]]
annotate[[annotate:\nAnnotate VCF against given\nreference VCF such as \n dbSNP, and rename any unknown\nvariants.]]
```

<dl>
Expand Down Expand Up @@ -314,6 +314,39 @@ normalize[[normalize:\nNormalize all SNPs]]

</details>

<details markdown="block">
<summary>
<code>annotateUnknown</code>
</summary>

```mermaid
flowchart TD
annotateUnknown[[annotateUnknown:\nName all un-annotated variants using \nstandardized naming conventions.]]
```

<dl>
<dt>Function</dt>
<dd>
To name all un-named variants which did not have a matching annotation ID.</dd>
<dt>Command</dt>
<dd><code>plink --vcf {input.vcf} --set-missing-var-ids @:#\$1-\$2 --new-id-max-allele-len 200 --out {params.output}</code></dd>
<dt>Parameters</dt>
<dd>
<dl>
<dt><code>--vcf {input.vcf}</code></dt>
<dd>File path to the input VCF file via parameter.</dd>
<dt><code>--set-missing-var-ids @:#\$1-\$2</code></dt>
<dd>A string which describes a naming scheme to be used when setting all un-named variants <code>@</code> denotes the chromosome code, <code>#</code> denotes the base-pair coordinates, <code>$1</code> denotes the reference allele and <code>$2</code> denotes the alternate allele.</dd>
<dt><code>--new-id-max-allele-len 200</code></dt>
<dd>Sets a maximum allowed variant ID length.</dd>
<dt><code>--out {params.output}</code></dt>
<dd>Provide the file name and path for output creation.</dd>
</dl>
</dd>
</dl>

</details>


<details markdown="block">
<summary>
Expand All @@ -322,17 +355,17 @@ normalize[[normalize:\nNormalize all SNPs]]

```mermaid
flowchart TD
subgraph liftoverProtocol [Liftover]
direction LR
liftoverProtocolStart(((Start)))
liftover[[liftover:\nPerform reference genome\nliftover]]
liftoverProtocolEnd(((End)))
ifLiftoverRequired{Is a\nliftover\nrequired?}
liftoverProtocolStart --> ifLiftoverRequired
ifLiftoverRequired --> |yes| liftover --> liftoverProtocolEnd
ifLiftoverRequired --> |no| liftoverProtocolEnd
end
subgraph liftoverProtocol [Liftover]
direction LR
liftoverProtocolStart(((Start)))
liftover[[liftover:\nPerform reference genome\nliftover]]
liftoverProtocolEnd(((End)))
ifLiftoverRequired{Is a\nliftover\nrequired?}
liftoverProtocolStart --> ifLiftoverRequired
ifLiftoverRequired --> |yes| liftover --> liftoverProtocolEnd
ifLiftoverRequired --> |no| liftoverProtocolEnd
end
```

<dl>
Expand Down Expand Up @@ -369,17 +402,17 @@ normalize[[normalize:\nNormalize all SNPs]]

```mermaid
flowchart TD
subgraph multipleVcfProtocol [Multiple dataset protocol]
direction LR
multipleVcfProtocolStart(((Start)))
ifMergeRequired{Is a \nmerge needed?}
mergeDatasets[[mergeDatasets:\nMerge multiple incoming\ndatasets]]
multipleVcfProtocolEnd(((End)))
multipleVcfProtocolStart --> ifMergeRequired
ifMergeRequired --> |yes| mergeDatasets --> multipleVcfProtocolEnd
ifMergeRequired --> |No| multipleVcfProtocolEnd
end
subgraph multipleVcfProtocol [Multiple dataset protocol]
direction LR
multipleVcfProtocolStart(((Start)))
ifMergeRequired{Is a \nmerge needed?}
mergeDatasets[[mergeDatasets:\nMerge multiple incoming\ndatasets]]
multipleVcfProtocolEnd(((End)))
multipleVcfProtocolStart --> ifMergeRequired
ifMergeRequired --> |yes| mergeDatasets --> multipleVcfProtocolEnd
ifMergeRequired --> |No| multipleVcfProtocolEnd
end
```
{: .normal }
> This rule only executes when multiple described datasets are detected. This rule is responsible for merging multiple datasets into a single VCF file, suitable for collective analysis.
Expand Down Expand Up @@ -410,7 +443,7 @@ normalize[[normalize:\nNormalize all SNPs]]

```mermaid
flowchart TD
refFromFasta[[refFromfasta:\nCheck reference alleles against\nprovided reference genome]]
refFromFasta[[refFromfasta:\nCheck reference alleles against\nprovided reference genome]]
```

<dl>
Expand Down Expand Up @@ -447,7 +480,7 @@ normalize[[normalize:\nNormalize all SNPs]]

```mermaid
flowchart TD
chrFilter[[chrFilter:\nFilter out non-standard\nchromosomes]]
chrFilter[[chrFilter:\nFilter out non-standard\nchromosomes]]
```

<dl>
Expand Down Expand Up @@ -485,7 +518,7 @@ normalize[[normalize:\nNormalize all SNPs]]

```mermaid
flowchart TD
filterRequestedSamples[[filterRequestedSamples:\nSubset samples to labeled\nsamples in metadata files]]
filterRequestedSamples[[filterRequestedSamples:\nSubset samples to labeled\nsamples in metadata files]]
```

<dl>
Expand Down Expand Up @@ -517,7 +550,7 @@ normalize[[normalize:\nNormalize all SNPs]]

```mermaid
flowchart TD
filterVariantMissingness[[filterVariantMissingness:\nFilter variants with 100%\nmissingness]]
filterVariantMissingness[[filterVariantMissingness:\nFilter variants with 100%\nmissingness]]
```

<dl>
Expand Down Expand Up @@ -556,7 +589,7 @@ normalize[[normalize:\nNormalize all SNPs]]

```mermaid
flowchart TD
filterSampleMissingness[[filterSampleMissingness:\nFilter samples with 100%\nmissingness]]
filterSampleMissingness[[filterSampleMissingness:\nFilter samples with 100%\nmissingness]]
```

<dl>
Expand Down Expand Up @@ -595,7 +628,7 @@ normalize[[normalize:\nNormalize all SNPs]]

```mermaid
flowchart TD
calculateLinkageDisequilibrium[[calculateLinkageDisequilibrium:\nCalculate LD associations]]
calculateLinkageDisequilibrium[[calculateLinkageDisequilibrium:\nCalculate LD associations]]
```

<dl>
Expand Down Expand Up @@ -634,7 +667,7 @@ normalize[[normalize:\nNormalize all SNPs]]

```mermaid
flowchart TD
filterLinkageDisequilibrium[[filterLinkageDisequilibrium:\nRemove variants in LD]]
filterLinkageDisequilibrium[[filterLinkageDisequilibrium:\nRemove variants in LD]]
```

<dl>
Expand Down Expand Up @@ -669,7 +702,7 @@ normalize[[normalize:\nNormalize all SNPs]]

```mermaid
flowchart TD
calculateIdentityByDescent[[calculateIdentityByDescent:\nCalculate Identity-By-Descent]]
calculateIdentityByDescent[[calculateIdentityByDescent:\nCalculate Identity-By-Descent]]
```

<dl>
Expand Down Expand Up @@ -708,7 +741,7 @@ normalize[[normalize:\nNormalize all SNPs]]

```mermaid
flowchart TD
calculateSampleIds[[calculateSampleIds:\nQuery a list of sample IDs\nfrom the input VCF]]
calculateSampleIds[[calculateSampleIds:\nQuery a list of sample IDs\nfrom the input VCF]]
```

<dl>
Expand All @@ -735,7 +768,7 @@ normalize[[normalize:\nNormalize all SNPs]]

```mermaid
flowchart TD
filterSampleRelatedness[[filterSampleRelatedness:\nremove a given list of samples\nbased on IBD results]]
filterSampleRelatedness[[filterSampleRelatedness:\nremove a given list of samples\nbased on IBD results]]
```

<dl>
Expand Down Expand Up @@ -766,7 +799,7 @@ normalize[[normalize:\nNormalize all SNPs]]

```mermaid
flowchart TD
filterLocations[[filterLocations:\nTrim the dataset to one of\nthe studied regions]]
filterLocations[[filterLocations:\nTrim the dataset to one of\nthe studied regions]]
```

<dl>
Expand Down Expand Up @@ -807,7 +840,7 @@ normalize[[normalize:\nNormalize all SNPs]]

```mermaid
flowchart TD
writeSampleMetadata[[writeSampleMetadata:\nTranspile cluster ownership from\nsample cluster assignment into\ninput format]]
writeSampleMetadata[[writeSampleMetadata:\nTranspile cluster ownership from\nsample cluster assignment into\ninput format]]
```

<dl>
Expand All @@ -834,7 +867,7 @@ normalize[[normalize:\nNormalize all SNPs]]

```mermaid
flowchart TD
reportFreq[[reportFreq:\nPerform frequency analysis]]
reportFreq[[reportFreq:\nPerform frequency analysis]]
```

<dl>
Expand Down Expand Up @@ -880,7 +913,7 @@ normalize[[normalize:\nNormalize all SNPs]]

```mermaid
flowchart TD
plinkPed[[plinkPed:\nConvert to PLINK-1.9's PED\n format]]
plinkPed[[plinkPed:\nConvert to PLINK-1.9's PED\n format]]
```

</details>
Expand All @@ -892,7 +925,7 @@ normalize[[normalize:\nNormalize all SNPs]]

```mermaid
flowchart TD
fetchPedLables[[fetchPedLables:\nGenerate Ind2Pop sample annotations\n file]]
fetchPedLables[[fetchPedLables:\nGenerate Ind2Pop sample annotations\n file]]
```

</details>
Expand All @@ -904,7 +937,7 @@ normalize[[normalize:\nNormalize all SNPs]]

```mermaid
flowchart TD
Admixture[[Admixture:\nPerform an admixture analysis]]
Admixture[[Admixture:\nPerform an admixture analysis]]
```

</details>
Expand All @@ -916,7 +949,7 @@ normalize[[normalize:\nNormalize all SNPs]]

```mermaid
flowchart TD
plinkPca[[Plink_PCA:\nPerform a PLINK-2.0 PCA]]
plinkPca[[Plink_PCA:\nPerform a PLINK-2.0 PCA]]
```

</details>
Expand Down

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