From 4027951ad65a310ce3f06f41941014fce2aa8a87 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 27 Oct 2022 16:33:35 +0200
Subject: [PATCH] doc/getting_started.md: fix typo :82
---
doc/getting_started.md | 8 +++++---
1 file changed, 5 insertions(+), 3 deletions(-)
diff --git a/doc/getting_started.md b/doc/getting_started.md
index 8a601a98..3b62c7a3 100644
--- a/doc/getting_started.md
+++ b/doc/getting_started.md
@@ -79,7 +79,7 @@ If the containers are not found locally, they are automatically downloaded befor
To have access to `charliecloud` on the PSMN you need to add the followin path to your `PATH` variable:
-````
+```sh
PATH=/Xnfs/abc/charliecloud_bin/:$PATH
```
@@ -87,7 +87,6 @@ You can add this line in your `~/.bashrc` or `~/.zshrc` file
When running `nextflow` on the PSMN, we recommend to use `tmux` before launching the pipeline:
-
```sh
tmux
./nextflow src/solution_RNASeq.nf --fastq "data/tiny_dataset/fastq/tiny2_R{1,2}.fastq.gz" --fasta "data/tiny_dataset/fasta/tiny_v2_10.fasta" --bed "data/tiny_dataset/annot/tiny.bed" -profile psmn
@@ -104,4 +103,7 @@ You can edit the `src/ccin2p3.pbs` file to personalize your `nextflow` command a
```sh
qsub src/ccin2p3.pbs
```
-````
+
+```
+
+```
--
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