Commit 6cbd129f authored by Midoux Cedric's avatar Midoux Cedric
Browse files

path/to/workflow

parent e99dc94e
......@@ -6,8 +6,8 @@ mkdir -p ./.log/out/ ./.log/err/
snakemake \
--snakefile $1 \
--jobscript jobscript.sh \
--cluster-config cluster.json \
--jobscript ../workflow_metagenomics/jobscript.sh \
--cluster-config ../workflow_metagenomics/cluster.json \
--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 \
......
......@@ -4,8 +4,8 @@ source activate snakemake-5.4.5
snakemake \
--snakefile $1 \
--jobscript jobscript.sh \
--cluster-config cluster.json \
--jobscript ../workflow_metagenomics/jobscript.sh \
--cluster-config ../workflow_metagenomics/cluster.json \
--dryrun \
--forceall \
--printshellcmds \
......
......@@ -4,8 +4,8 @@ source activate snakemake-5.4.5
snakemake \
--snakefile $1 \
--jobscript jobscript.sh \
--cluster-config cluster.json \
--jobscript ../workflow_metagenomics/jobscript.sh \
--cluster-config ../workflow_metagenomics/cluster.json \
--dryrun \
--printshellcmds \
--verbose
......@@ -6,7 +6,7 @@ mkdir -p report/
snakemake \
--snakefile $1 \
--jobscript jobscript.sh \
--cluster-config cluster.json \
--jobscript ../workflow_metagenomics/jobscript.sh \
--cluster-config ../workflow_metagenomics/cluster.json \
--report report/`basename $1 .smk`_report.html \
--verbose
shell.executable("/bin/bash")
shell.prefix("source ~/.bashrc; "
shell.prefix("source ~/.bashrc; ")
import os
configfile: "./config.json"
SAMPLES=config["SAMPLES"]
rule all:
input:
"",
......
mkdir -p ./.log/out/ ./.log/err/
qsub -V -cwd -o ./.log/out/ -e ./.log/err/ -q maiage.q,long.q -N `basename $1` RunSnake.sh $1
qsub -V -cwd -o ./.log/out/ -e ./.log/err/ -q maiage.q,long.q -N `basename $1` ../workflow_metagenomics/RunSnake.sh $1
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