From a0949542a418576a4e3b6c61407f0d24bedc9f2c Mon Sep 17 00:00:00 2001
From: Monica Ticlla <monicaroxana.ticllaccenhua@unibas.ch>
Date: Fri, 20 Nov 2020 19:12:09 +0100
Subject: [PATCH] minor edits in step3
---
README.md | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/README.md b/README.md
index 53d69fa..e861e9a 100644
--- a/README.md
+++ b/README.md
@@ -202,7 +202,7 @@ Execute the workflow **locally** via
snakemake \
--profile $metasnk/profiles/local \
--cores $N \
- --directory='<path_to/my_working_directory>' \
+ --directory <path_to/my_working_directory> \
-s $metasnk/Snakefile <METASNK_MODULE>
using `$N` cores, and specifying a **working directory**. Have in mind that the working directory is where MetaSnk will try to find your configuration file and also it is where snakemake will store files to track the status of a running MetaSnk workflow.
@@ -213,7 +213,7 @@ or, **in a cluster environment controlled by SLURM** workload manager via
--profile $metasnk/profiles/slurm \
--cores $N \
--cluster-config $metasnk/slurm_cluster.json \
- --directory='<path_to/my_working_directory>' \
+ --directory <path_to/my_working_directory> \
-s $metasnk/Snakefile <METASNK_MODULE>
See the [Snakemake documentation](https://snakemake.readthedocs.io/en/stable/executable.html) for further details.
@@ -223,13 +223,13 @@ See the [Snakemake documentation](https://snakemake.readthedocs.io/en/stable/exe
After successful execution, you can create a self-contained interactive HTML report with all results via:
snakemake \
- --directory='<path_to/my_working_directory>' \
+ --directory <path_to/my_working_directory> \
-s $metasnk/Snakefile rawQC_make_report
or
snakemake \
- --directory='<path_to/my_working_directory>' \
+ --directory <path_to/my_working_directory> \
-s $metasnk/Snakefile preQC_make_report
These reports can, e.g., be forwarded to your collaborators.
--
GitLab