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docs: Update backend docs for DNAnexus, and update script for updating docs.
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‎docs/backend-dnanexus.md‎

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The PacBio Human WGS Variant Pipeline is an analysis workflow for PacBio HiFi human whole genome sequencing data, with joint calling for related samples.
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Templates and instructions for how to submit the `family` input on the DNAnexus platform are provided in the [Example JSON Documents](#example-json-documents) and [Submitting to DNAnexus](#submitting-to-dnanexus) sections below.
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Templates and instructions for how to submit the `Family struct` input on the DNAnexus platform are provided in the [Example JSON Documents](#example-json-documents) and [Submitting to DNAnexus](#submitting-to-dnanexus) sections below.
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## Inputs
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The workflow has the following inputs:
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| Type | Name | Description | Notes |
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| ---- | ---- | ----------- | ----- |
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| Struct | family | Family struct describing samples, relationships, and unaligned BAM paths. | See below for more information |
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| String | phenotypes | [Human Phenotype Ontology](https://hpo.jax.org/) (HPO) phenotypes associated with the affected proband. | For example, if the proband has seizures and hypotonia, then the `phenotypes` string might be `"HP:0001250,HP:0001252"`. |
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| File | trgt_tandem_repeat_bed | BED file containing repeat coordinates and information about the repeat structure | The default file should be sufficient for most use cases |
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| Integer | glnexus_mem_gb | Override GLnexus memory request (GB) | Optional. Should only be specified if GLnexus step fails. |
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| Integer | pbsv_call_mem_gb | Override PBSV call memory request (GB) | Optional. Should only be specified if PBSV step fails. |
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| Boolean | run_tertiary | Whether to run tertiary analysis for small variants and structural variants | Default: `true` |
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| File chooser | Family struct | One or more files corresponding to the sample data described in your Family struct JSON below. |
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| File chooser | TRGT Tandem Repeat Definitions | BED file containing repeat coordinates and information about the repeat structure. | The default file should be sufficient for most use cases. |
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| Struct | Family struct | Family struct JSON describing samples, relationships, and unaligned BAM paths. | See below for more information. |
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| Integer | GLnexus memory override | Override GLnexus memory request (GB) | Optional. Should only be specified if GLnexus step fails. |
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| Integer | PBSV memory override | Override PBSV call memory request (GB) | Optional. Should only be specified if PBSV step fails. |
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| String | Phenotypes | [Human Phenotype Ontology](https://hpo.jax.org/) Comma-delimited string of (HPO) phenotypes associated with the affected proband. | For example, if the proband has seizures and hypotonia, then the `phenotypes` string would be `HP:0001250,HP:0001252`. |
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| Boolean | Run tertiary analysis | Whether to run tertiary analysis for small variants and structural variants | Default: `true` |
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## Family Struct Syntax
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The `Family` input for the HiFi-human-WGS-WDL workflow is a JSON document that contains the samples for the family. The same struct is used for a single sample or trio, with the single sample case having only one entry in the `samples` array.
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The `Family` input for the HiFi-human-WGS-WDL workflow is a JSON document that contains the samples for the family. The same struct syntax is used for a single sample or trio, with the single sample case having only one entry in the `samples` array.
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### Structs and Field Descriptions
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```json
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{
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"family": {
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"family_id": "AJTRIO",
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"samples": [
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{
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"sample_id": "HG002",
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"hifi_reads": [
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{
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"$dnanexus_link": {
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"id": "file-xxxx",
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"project": "project-xxxx"
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}
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"family_id": "AJTRIO",
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"samples": [
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{
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"sample_id": "HG002",
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"hifi_reads": [
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{
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"$dnanexus_link": {
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"id": "file-xxxx",
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"project": "project-xxxx"
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}
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],
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"affected": true,
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"sex": "MALE",
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"father_id": "HG003",
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"mother_id": "HG004"
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},
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{
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"sample_id": "HG003",
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"hifi_reads": [
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{
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"$dnanexus_link": {
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"id": "file-xxxx",
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"project": "project-xxxx"
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}
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}
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],
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"affected": true,
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"sex": "MALE",
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"father_id": "HG003",
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"mother_id": "HG004"
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},
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{
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"sample_id": "HG003",
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"hifi_reads": [
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{
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"$dnanexus_link": {
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"id": "file-xxxx",
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"project": "project-xxxx"
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}
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],
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"affected": false,
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"sex": "MALE"
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},
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{
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"sample_id": "HG004",
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"hifi_reads": [
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{
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"$dnanexus_link": {
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"id": "file-xxxx",
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"project": "project-xxxx"
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}
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}
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],
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"affected": false,
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"sex": "MALE"
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},
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{
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"sample_id": "HG004",
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"hifi_reads": [
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{
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"$dnanexus_link": {
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"id": "file-xxxx",
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"project": "project-xxxx"
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}
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],
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"affected": false,
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"sex": "FEMALE"
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}
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]
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}
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}
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],
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"affected": false,
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"sex": "FEMALE"
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}
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]
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}
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```
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‎scripts/update_docs.sh‎

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# create a README.md file from the Home.md file in the wiki directory
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# with correct relative links
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sed 's!(\./!(./docs/!g;s!\.\./\.\.!../../..!g;' "$1"/Home.md > README.md
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cp "$1"/*.md docs/
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rm docs/Home.md docs/_Sidebar.md
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sed 's!(\./docs/!(./!g;s!\.\./\.\./\.\.!../..!g;' README.md > "$1"/Home.md
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cp docs/*.md "$1"/

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