From d1dedffd086152de704a518fcbd468f253daba56 Mon Sep 17 00:00:00 2001 From: Fredrik Boulund Date: Wed, 5 Apr 2023 13:39:34 +0200 Subject: [PATCH] Clarify how to specify the samplesheet on the commandline --- config/README.md | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/config/README.md b/config/README.md index 8b85cbb..62e94d8 100644 --- a/config/README.md +++ b/config/README.md @@ -44,6 +44,14 @@ anywhere, i.e. their locations are not restricted to the repository folder and they can even be located in remote storage systems like S3 or a public HTTP URL. +If the samplesheet setting is configured in the `config/config.yaml` file, or +provided on the command line when running by utilizing Snakemake’s built-in +functionality for modifying configuration settings via the command line +directive `--config samplesheet=path/to/samplesheet.tsv`, it will override any +input folder settings configured in the `config/config.yaml` file. + + + ## Select which tools to run Next, configure the settings under the `Pipeline steps included` heading. This is where you define what steps should be included in your workflow. Simply