From 503a955a832c0896cf796d95c1d78742e1895fb3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Karel=20B=C5=99inda?= Date: Wed, 6 Mar 2024 15:18:20 +0100 Subject: [PATCH] Document passing cluster-related smk params --- README.md | 30 +++++++++++++++++++++--------- 1 file changed, 21 insertions(+), 9 deletions(-) diff --git a/README.md b/README.md index 22211e6..e7fbc36 100644 --- a/README.md +++ b/README.md @@ -30,15 +30,16 @@ and the associated paper * [1. Introduction](#1-introduction) * [2. Dependencies](#2-dependencies) - * [2a. Essential dependencies](#2a-essential-dependencies) - * [2b. Protocol-specific dependencies](#2b-protocol-specific-dependencies) + * [2a. Essential dependencies](#2a-essential-dependencies) + * [2b. Protocol-specific dependencies](#2b-protocol-specific-dependencies) * [3. Installation](#3-installation) * [4. Usage](#4-usage) - * [4a. Basic example](#4a-basic-example) - * [4b. Adjusting configuration](#4b-adjusting-configuration) - * [4c. List of implemented protocols](#4c-list-of-implemented-protocols) - * [4d. List of workflow commands](#4d-list-of-workflow-commands) - * [4e. Troubleshooting](#4e-troubleshooting) + * [4a. Basic example](#4a-basic-example) + * [4b. Adjusting configuration](#4b-adjusting-configuration) + * [4c. List of implemented protocols](#4c-list-of-implemented-protocols) + * [4d. List of workflow commands](#4d-list-of-workflow-commands) + * [4e. Running on a cluster.](#4e-running-on-a-cluster) + * [4f. Troubleshooting](#4f-troubleshooting) * [5. Citation](#5-citation) * [6. Issues](#6-issues) * [7. Changelog](#7-changelog) @@ -286,9 +287,20 @@ Here's a list of all implemented commands (to be executed as `make {command}`): `conda install -c conda-forge -bioconda yapf snakefmt`. -### 4e. Troubleshooting -Tests can be run by `make test`. +### 4e. Running on a cluster. + +Cluster-related parameters for Snakemake can be added via the `SMK_CLUSTER_ARGS` Make variable. + +Example: +```bash + make SMK_CLUSTER_ARGS="--profile my_snakemake_cluster_profile" +``` + + +### 4f. Troubleshooting + +Tests can be run by `make test` (just Protocol 1) or `make bigtest` (all the protocols). ## 5. Citation