From 2fbc38f6df7a802d33e816bf61fc0a5c645fb50a Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Thu, 5 Nov 2020 11:16:22 +0100
Subject: [PATCH] Fix markdownlint errors
---
README.md | 12 +++++++-----
1 file changed, 7 insertions(+), 5 deletions(-)
diff --git a/README.md b/README.md
index cd476c6..36b30b2 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
```
--
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