diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 4252b0d63..c312cb3a5 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -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: diff --git a/CHANGELOG.md b/CHANGELOG.md index 79b1c3546..bc790b0c2 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -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 diff --git a/docs/usage.md b/docs/usage.md index 4d2cd4e1c..14c48d4ba 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -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 | base64 -w 0) ``` +:::note + 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 | 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.