diff --git a/CADD.sh b/CADD.sh index 8b33cbb..8721ff7 100755 --- a/CADD.sh +++ b/CADD.sh @@ -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 diff --git a/Snakefile b/Snakefile index 24f3af6..90317bf 100644 --- a/Snakefile +++ b/Snakefile @@ -20,7 +20,7 @@ import os envvars: "CADD", - +localrules: decompress, prepare, prescore, annotation_vep, annotate_regseq, annotate_mmsplice, annotation, imputation, score, join # START Rules