Add example of overriding cluster config defaults

code/myworkflow.smk

@@ -2,12 +2,27 @@ samples, = glob_wildcards("data/sample_{sample}.txt")
 
 rule targets:
 	input:
-		expand("results/result_{sample}.txt", sample = samples)	
+		expand("results/sample_{sample}_sleep.txt", sample = samples)	
 
 rule copy:
 	input:
-		"data/sample_{sample}.txt"
+		txt="data/sample_{sample}.txt"
 	output:
-		"results/result_{sample}.txt"
+		txt="results/sample_{sample}_copy.txt"
 	shell:
 		"cp {input} {output}"
+
+rule sleep:
+        input:
+                rules.copy.output.txt
+        output:
+                "results/sample_{sample}_sleep.txt"
+        shell:
+                """
+                echo "Imagine that this is a job with more intensive resource requirements..."
+                time sleep 5s > {output}
+                """
+
+rule clean:
+        shell:
+                "rm results/*"

code/submit-pbs.sh

@@ -7,7 +7,7 @@
 #PBS -m abe                ## when to send email a=abort b=job begin e=job end
 #PBS -j oe                 ## send output and error information to the email listed above
 #PBS -V                 ## IMPORTANT always use this. send environment setup to node job will be run on
-#PBS -o logfiles/  ## write output/error logfile(s) to this dir
+#PBS -o log/hpc  ## write output/error logfile(s) to this dir
 #
 #  Include the next three lines always
 if [ "x${PBS_NODEFILE}" != "x" ] ; then

code/submit-slurm.sh

@@ -34,4 +34,7 @@
 #SBATCH --mail-user=your_email
 #SBATCH --mail-type=BEGIN,END
 
+#### where to write log files
+
+#SBATCH --output=log/hpc/
 snakemake --profile config/slurm --latency-wait 20 -s code/myworkflow.smk

config/cluster.json

@@ -13,5 +13,9 @@
     "mailon": "a",
     "mail_type": "FAIL",
     "jobout": "oe",
-    "outdir": "logfiles/hpc/"
+    "outdir": "log/hpc/"
+}
+"sleep": {
+    "walltime": "24:00:00",
+    "pmem": "2GB"
 }