Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

note on '--tools' in Quickstart #1166

Merged
merged 5 commits into from
Aug 15, 2023
Merged

note on '--tools' in Quickstart #1166

Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
6ec8c1c
Merge pull request #1096 from nf-core/dev
asp8200 Jun 15, 2023
ed1cc84
Merge pull request #1129 from nf-core/dev
asp8200 Jun 22, 2023
1bd3637
note on '--tools' in Quickstart
ATpoint Jul 28, 2023
7175be3
[automated] Fix linting with Prettier
nf-core-bot Jul 28, 2023
0ba4cf5
Merge branch 'dev' into master
maxulysse Aug 15, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
5 changes: 3 additions & 2 deletions docs/usage.md
View file
Open in desktop
Original file line number Diff line number Diff line change
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:

Expand Down