diff --git a/README.md b/README.md index cd476c6432b7b1f9290d41a939c268c1de296d04..36b30b284d5422dce15ce8bfd4498e97b66fd37d 100644 --- a/README.md +++ b/README.md @@ -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 ```