global.smk

RunSnake.sh

@@ -11,8 +11,6 @@ snakemake \
 --cluster "qsub -V -cwd -R y -N {rule} -o {cluster.out} -e {cluster.err} -q {cluster.queue} -pe thread {threads} {cluster.cluster}" \
 --keep-going \
 --jobs 80 \
---use-conda \
---conda-prefix /projet/maiage/save/cmidoux/environments/ \
 --wait-for-files \
 --latency-wait 150 \
 --use-conda \

cluster.json

@@ -36,5 +36,4 @@
 		"queue" : "highmem.q,maiage.q",
 		"cluster" : "-l h_vmem={MEM}G"
 	}
-
 }

global.smk

+shell.executable("/bin/bash")
+shell.prefix("source ~/.bashrc; "
+
+import os
+configfile: "./config.json"
+
+SAMPLES=config["SAMPLES"]
+
+rule all:
+	input:
+		"",
+
+include: "../workflow_metagenomics/*.smk"