Commit e99dc94e authored by Midoux Cedric's avatar Midoux Cedric
Browse files

global.smk

parent e1a25923
......@@ -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 \
......
......@@ -36,5 +36,4 @@
"queue" : "highmem.q,maiage.q",
"cluster" : "-l h_vmem={MEM}G"
}
}
shell.executable("/bin/bash")
shell.prefix("source ~/.bashrc; "
import os
configfile: "./config.json"
SAMPLES=config["SAMPLES"]
rule all:
input:
"",
include: "../workflow_metagenomics/*.smk"
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