Improve help messages

Makefile

@@ -38,12 +38,17 @@ BIG_TEST_PARAMS = --config protocol_pre=True protocol_post=True
 ## General commands ##
 ######################
 
-all: ## Run everything
+all: ## Run everything (the default subcommand)
 	snakemake $(SNAKEMAKE_PARAMS)
 
 help: ## Print help messages
-	@echo "$$(grep -hE '^\S*(:.*)?##' $(MAKEFILE_LIST) \
-		| sed -e 's/:.*##\s*/:/' -e 's/^\(.\+\):\(.*\)/\\x1b[36m\1\\x1b[m:\2/' -e 's/^\([^#]\)/    \1/g'\
+	@echo -e "$$(grep -hE '^\S*(:.*)?##' $(MAKEFILE_LIST) \
+		| sed \
+			-e 's/:.*##\s*/:/' \
+			-e 's/^\(.*\):\(.*\)/   \\x1b[36m\1\\x1b[m:\2/' \
+			-e 's/^\([^#]\)/\1/g' \
+			-e 's/: /:/g' \
+			-e 's/^#\(.*\)#/\\x1b[90m\1\\x1b[m/' \
 		| column -c2 -t -s : )"
 
 conda: ## Create the conda environments
@@ -99,15 +104,13 @@ test: ## Run the workflow on test data (P1)
 		snakemake $(SNAKEMAKE_PARAMS); \
 	fi
 
-
 bigtest: ## Run the workflow on test data (P1, P2, P3)
 	if [ -d ".test" ]; then \
 		$(MAKE) -C .test bigtest; \
 	else\
 		snakemake $(SNAKEMAKE_PARAMS) $(BIG_TEST_PARAMS); \
 	fi
 
-
 format: ## Reformat all source code
 	snakefmt workflow
 	yapf -i --recursive workflow

README.md

@@ -262,7 +262,7 @@ Here's a list of all implemented commands (to be executed as `make {command}`):
 ######################
 ## General commands ##
 ######################
-    all                  Run everything
+    all                  Run everything (the default subcommand)
     help                 Print help messages
     conda                Create the conda environments
     clean                Clean all output archives and files with statistics
@@ -276,7 +276,8 @@ Here's a list of all implemented commands (to be executed as `make {command}`):
 ####################
 ## For developers ##
 ####################
-    test                 Run the workflow on test data
+    test                 Run the workflow on test data (P1)
+    bigtest              Run the workflow on test data (P1, P2, P3)
     format               Reformat all source code
     checkformat          Check source code format
 ```
@@ -291,9 +292,10 @@ Here's a list of all implemented commands (to be executed as `make {command}`):
 ### 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"
+make SMK_CLUSTER_ARGS="--profile my_snakemake_cluster_profile"
 ```