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Add cluster configuration for CADD pipeline #49

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Add cluster configuration for CADD pipeline #49

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7 changes: 6 additions & 1 deletion CADD.sh
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Expand Up @@ -120,11 +120,16 @@ TMP_OUTFILE=$TMP_FOLDER/$NAME.tsv.gz

cp $INFILE $TMP_INFILE

mkdir -p $CADD/logs

echo "Running snakemake pipeline:"
echo snakemake $TMP_OUTFILE --use-conda --conda-prefix $CADD/envs/conda --cores $CORES
echo --configfile $CONFIG --snakefile $CADD/Snakefile $VERBOSE
echo --cluster-cancel scancel --cluster-status status.py --cluster \"sbatch --parsable --nodes=1 --ntasks=1 --mem=20G -t '01-00:00' -p gpu --gres=gpu:1 -o $CADD/logs\"

snakemake $TMP_OUTFILE --use-conda --conda-prefix $CADD/envs/conda --cores $CORES \
--configfile $CONFIG --snakefile $CADD/Snakefile $VERBOSE
--configfile $CONFIG --snakefile $CADD/Snakefile $VERBOSE \
--cluster-cancel scancel --cluster-status status.py --cluster "sbatch --parsable --nodes=1 --ntasks=1 --mem=20G -t '01-00:00' -p gpu --gres=gpu:1 -o $CADD/logs"

mv $TMP_OUTFILE $OUTFILE
rm $TMP_INFILE # is in temp folder, should not be necessary
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2 changes: 1 addition & 1 deletion Snakefile
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Expand Up @@ -20,7 +20,7 @@ import os
envvars:
"CADD",


localrules: decompress, prepare, prescore, annotation_vep, annotate_regseq, annotate_mmsplice, annotation, imputation, score, join
# START Rules


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