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Update Sentieon Docs #1579

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Update Sentieon Docs #1579

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e4475d2
docs: Add note about Sentieon license string
edmundmiller Jul 1, 2024
cc46af9
docs: Link to README for Sentieon License server
edmundmiller Jul 1, 2024
25fc83b
ci: Avoid running tests on docs
edmundmiller Jul 1, 2024
c332140
chore: Update Changelog
edmundmiller Sep 19, 2024
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2 changes: 2 additions & 0 deletions .github/workflows/ci.yml
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Expand Up @@ -2,6 +2,8 @@ name: nf-core CI
# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
on:
pull_request:
paths-ignore:
- "docs/**"
release:
types: [published]
merge_group:
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -14,6 +14,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### Changed

- [1579](https://github.com/nf-core/sarek/pull/1579) - Update Sentieon usage docs

### Fixed

- [1657](https://github.com/nf-core/sarek/pull/1657) - Update all actions used in the GHA CI
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8 changes: 8 additions & 0 deletions docs/usage.md
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Expand Up @@ -1100,12 +1100,20 @@ Sentieon supply license in the form of a string-value (a url) or a file. It shou
nextflow secrets set SENTIEON_LICENSE_BASE64 $(echo -n <sentieon_license_string> | base64 -w 0)
```

:::note
<sentieon_license_string> is formatted as `IP:Port` for example: `12.12.12.12:8990`
:::

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)
```

:::note
If you're looking for documentation on how the nf-core Sentieon GitHub Actions and Sentieon License Server are set up: [Here be dragons.](https://github.com/nf-core/ops/blob/main/pulumi/aws_license-server/README.md)
:::

### Available Sentieon functions

Sarek contains the following Sentieon functions from [DnaSeq](https://support.sentieon.com/manual/DNAseq_usage/dnaseq/) : [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.
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