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Commit 2fbc38f6 authored by Phil Ewels's avatar Phil Ewels
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Fix markdownlint errors

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......@@ -47,17 +47,19 @@ sites (bowtie2)
2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/) or [`Podman`](https://podman.io/) for full pipeline reproducibility _(please only use [`Conda`](https://conda.io/miniconda.html) as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_
3. Download the pipeline and test it on a minimal dataset with a single command
```bash
nextflow run nf-core/hic -profile test,<docker/singularity/podman/conda/institute>
```
> Please check [nf-core/configs](https://github.com/nf-core/configs#documentation)
to see if a custom config file to run nf-core pipelines already exists for your Institute.
If so, you can simply use `-profile <institute>` in your command.
This will enable either `docker` or `singularity` and set the appropriate execution
settings for your local compute environment.
> Please check [nf-core/configs](https://github.com/nf-core/configs#documentation)
to see if a custom config file to run nf-core pipelines already exists for your Institute.
If so, you can simply use `-profile <institute>` in your command.
This will enable either `docker` or `singularity` and set the appropriate execution
settings for your local compute environment.
4. Start running your own analysis!
```bash
nextflow run nf-core/hic -profile <docker/singularity/podman/conda/institute> --input '*_R{1,2}.fastq.gz' --genome GRCh37
```
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