Merge pull request #106 from karel-brinda/cluster

Cluster

Makefile

@@ -23,8 +23,13 @@ ifeq ($(strip $(USE_CONDA)),True)
 	CONDA_PARAMS  =	--use-conda --conda-prefix="$(CONDA_DIR)"
 endif
 
-SNAKEMAKE_PARAMS = --cores $(THREADS) $(CONDA_PARAMS) --rerun-incomplete -p #--show-failed-logs
-
+ifeq ($(SMK_CLUSTER_ARGS),)
+    # configure local run
+	SNAKEMAKE_PARAMS = --cores $(THREADS) $(CONDA_PARAMS) --rerun-incomplete --printshellcmds #--show-failed-logs
+else
+    # configure cluster run
+	SNAKEMAKE_PARAMS = --cores all $(CONDA_PARAMS) $(SMK_CLUSTER_ARGS) --rerun-incomplete --printshellcmds #--show-failed-logs
+endif
 BIG_TEST_PARAMS = --config protocol_pre=True protocol_post=True
 
 

README.md

@@ -30,15 +30,16 @@ and the <a href="https://doi.org/10.1101/2023.04.15.536996">associated paper</a>
 
 * [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