From 5f57e16aacc9f6b0cfcbf6770cbf460f65c565f6 Mon Sep 17 00:00:00 2001
From: Max Schubach <max.schubach@bih-charite.de>
Date: Thu, 28 Dec 2023 20:11:54 +0100
Subject: [PATCH] Add cluster configuration for CADD pipeline

---
 CADD.sh   | 7 ++++++-
 Snakefile | 2 +-
 2 files changed, 7 insertions(+), 2 deletions(-)

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