diff --git a/README.md b/README.md index 53d69faf4fed6fc44f31a0b90e5068699564f6a8..e861e9ae6b78276c726ac8fd8f19f49e67afa122 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.