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maxulysse merged 5 commits into from
Aug 15, 2023
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note on '--tools' in Quickstart #1166

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6ec8c1c
Merge pull request #1096 from nf-core/dev
asp8200 Jun 15, 2023
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Merge pull request #1129 from nf-core/dev
asp8200 Jun 22, 2023
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note on '--tools' in Quickstart
ATpoint Jul 28, 2023
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[automated] Fix linting with Prettier
nf-core-bot Jul 28, 2023
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Merge branch 'dev' into master
maxulysse Aug 15, 2023
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5 changes: 3 additions & 2 deletions docs/usage.md
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Expand Up @@ -18,10 +18,11 @@ Sarek is designed to handle single samples, such as single-normal or single-tumo
The typical command for running the pipeline is as follows:

```bash
nextflow run nf-core/sarek --input ./samplesheet.csv --outdir ./results --genome GATK.GRCh38 -profile docker
nextflow run nf-core/sarek --input ./samplesheet.csv --outdir ./results --genome GATK.GRCh38 --tools <TOOLS> -profile docker
```

This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles.
This will launch the pipeline and perform variant calling with the tools specified in `--tools`, see the [parameter section](https://nf-co.re/sarek/3.2.3/parameters#tools) for details on variant calling tools.
In the above example the pipeline runs with the `docker` configuration profile. See below for more information about profiles.

Note that the pipeline will create the following files in your working directory:

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