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clean up sentieon docs split up
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@FriederikeHanssen
FriederikeHanssen committed Aug 17, 2023
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```

## Sentieon

[Sentieon](https://www.sentieon.com/) is a commercial solution to process genomics data with high computing efficiency, fast turnaround time, exceptional high accuracy, and 100% consistency.

In particular, Sentieon contains what may be view as speedup version of some standard GATK tools, like bwamem and haplotyper. Sarek contains support for some of the functions in Sentieon. In order to use those functions, the user will need to supply Sarek with a license for Sentieon.

### Setup of Sentieon license

Sentieon supply license in the form of a string-value (a url) or a file. It should be base64-encoded and stored in a nextflow secret named `SENTIEON_LICENSE_BASE64`. If a license string (url) is supplied, then the nextflow secret should be set like this:

```bash
nextflow secret set SENTIEON_LICENSE_BASE64 $(echo -n <sentieon_license_string> | base64 -w 0)
```

If a license file is supplied, then the nextflow secret should be set like this:

```bash
nextflow secrets set SENTIEON_LICENSE_BASE64 \$(cat <sentieon_license_file.lic> | base64 -w 0)
```

### Available Sentieon functions

Sarek contains the following Sentieon functions [bwa mem](https://support.sentieon.com/manual/usages/general/#bwa-mem-syntax), [LocusCollector](https://support.sentieon.com/manual/usages/general/#locuscollector-algorithm) + [Dedup](https://support.sentieon.com/manual/usages/general/#dedup-algorithm), [Haplotyper](https://support.sentieon.com/manual/usages/general/#haplotyper-algorithm), [GVCFtyper](https://support.sentieon.com/manual/usages/general/#gvcftyper-algorithm) and [VarCal](https://support.sentieon.com/manual/usages/general/#varcal-algorithm) + [ApplyVarCal](https://support.sentieon.com/manual/usages/general/#applyvarcal-algorithm), so the basic processing of alignment of fastq-files to VCF-files can be done using speedup Sentieon functions.

### Basic usage of Sentieon functions

To use Sentieon's aligner `bwa mem`, set the aligner option `sentieon-bwamem`. (This can, for example, be done by adding `--aligner sentieon-bwamem` to the nextflow run command.)

To use Sentieon's function `Dedup`, specify `sentieon_dedup` as one of the tools. (This can, for example, be done by adding `--tools sentieon_dedup` to the nextflow run command.)

To use Sentieon's function `Haplotyper`, specify `sentieon_haplotyper` as one of the tools. This can, for example, be done by adding `--tools sentieon_haplotyper` to the nextflow run command. In order to skip the GATK-based variant-filter, one may add `--skip_tools haplotyper_filter` to the nextflow run command. Sarek also provides the option `sentieon_haplotyper_emit_mode` which can be used to set the [emit-mode](https://support.sentieon.com/manual/usages/general/#haplotyper-algorithm) of Sentieon's haplotyper. Sentieon's haplotyper can output both a vcf-file and a gvcf-file in the same run; this is achieved by setting `sentieon_haplotyper_emit_mode` to `<vcf_emit_mode>,gvcf`, where `<vcf_emit_mode>` is `variant`, `confident` or `all`.

To use Sentieon's function `GVCFtyper` along with Sention's version of VQSR (`VarCal` and `ApplyVarCal`) for joint-germline genotyping, specify `sentieon_haplotyper` as one of the tools, set the option `sentieon_haplotyper_emit_mode` to `gvcf`, and add the option `joint_germline`. This can, for example, be done by adding `--tools sentieon_haplotyper --joint_germline --sentieon_haplotyper_emit_mode gvcf` to the nextflow run command.

## Updating the pipeline

When you launch a pipeline from the command-line with `nextflow run nf-core/sarek -profile docker -params-file params.yaml`, Nextflow will automatically pull the pipeline code from GitHub and store it as a cached version. When running the pipeline after this, it will always use the cached version if available - even if the pipeline has been updated since. To make sure that you're running the latest version of the pipeline, make sure that you regularly update the cached version of the pipeline:
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## Sentieon
[Sentieon](https://www.sentieon.com/) is a commercial solution to process genomics data with high computing efficiency, fast turnaround time, exceptional high accuracy, and 100% consistency.
In particular, Sentieon contains what may be view as speedup version of some standard GATK tools, like bwamem and haplotyper. Sarek contains support for some of the functions in Sentieon. In order to use those functions, the user will need to supply Sarek with a license for Sentieon.
### Setup of Sentieon license
Sentieon supply license in the form of a string-value (a url) or a file. It should be base64-encoded and stored in a nextflow secret named `SENTIEON_LICENSE_BASE64`. If a license string (url) is supplied, then the nextflow secret should be set like this:
```bash
nextflow secret set SENTIEON_LICENSE_BASE64 $(echo -n <sentieon_license_string> | base64 -w 0)
```
If a license file is supplied, then the nextflow secret should be set like this:
```bash
nextflow secrets set SENTIEON_LICENSE_BASE64 \$(cat <sentieon_license_file.lic> | base64 -w 0)
```
### Available Sentieon functions
Sarek contains the following Sentieon functions [bwa mem](https://support.sentieon.com/manual/usages/general/#bwa-mem-syntax), [LocusCollector](https://support.sentieon.com/manual/usages/general/#locuscollector-algorithm) + [Dedup](https://support.sentieon.com/manual/usages/general/#dedup-algorithm), [Haplotyper](https://support.sentieon.com/manual/usages/general/#haplotyper-algorithm), [GVCFtyper](https://support.sentieon.com/manual/usages/general/#gvcftyper-algorithm) and [VarCal](https://support.sentieon.com/manual/usages/general/#varcal-algorithm) + [ApplyVarCal](https://support.sentieon.com/manual/usages/general/#applyvarcal-algorithm), so the basic processing of alignment of fastq-files to VCF-files can be done using speedup Sentieon functions.
### Basic usage of Sentieon functions
To use Sentieon's aligner `bwa mem`, set the aligner option `sentieon-bwamem`. (This can, for example, be done by adding `--aligner sentieon-bwamem` to the nextflow run command.)
To use Sentieon's function `Dedup`, specify `sentieon_dedup` as one of the tools. (This can, for example, be done by adding `--tools sentieon_dedup` to the nextflow run command.)
To use Sentieon's function `Haplotyper`, specify `sentieon_haplotyper` as one of the tools. This can, for example, be done by adding `--tools sentieon_haplotyper` to the nextflow run command. In order to skip the GATK-based variant-filter, one may add `--skip_tools haplotyper_filter` to the nextflow run command. Sarek also provides the option `sentieon_haplotyper_emit_mode` which can be used to set the [emit-mode](https://support.sentieon.com/manual/usages/general/#haplotyper-algorithm) of Sentieon's haplotyper. Sentieon's haplotyper can output both a vcf-file and a gvcf-file in the same run; this is achieved by setting `sentieon_haplotyper_emit_mode` to `<vcf_emit_mode>,gvcf`, where `<vcf_emit_mode>` is `variant`, `confident` or `all`.
To use Sentieon's function `GVCFtyper` along with Sention's version of VQSR (`VarCal` and `ApplyVarCal`) for joint-germline genotyping, specify `sentieon_haplotyper` as one of the tools, set the option `sentieon_haplotyper_emit_mode` to `gvcf`, and add the option `joint_germline`. This can, for example, be done by adding `--tools sentieon_haplotyper --joint_germline --sentieon_haplotyper_emit_mode gvcf` to the nextflow run command.
### Joint germline variant calling
Sentieon's [GVCFtyper](https://support.sentieon.com/manual/usages/general/#gvcftyper-algorithm) does not support the [GenomicsDB](https://gatk.broadinstitute.org/hc/en-us/articles/5358869876891-GenomicsDBImport) datastore format. This means that, in contrast to the GATK based joint germline variant calling subworkflow in Sarek, the Sentieon/DNAseq based joint germline variant calling subworkflow does not use the GenomicsDB datastore format.
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