Update run_pipeline_cluster.sh to prevent the need to specify config an snakefile location.

run_pipeline_cluster.sh

@@ -10,16 +10,16 @@
 #$ -M b.f.tan@lumc.nl
 
 ##Create or update conda environment and activate it
-#conda-env update -n CNAprioritization -f envs/pipeline.yaml || conda-env create -n CNAprioritization -f envs/pipeline.yaml &&
+conda-env update -n CNAprioritization -f envs/pipeline.yaml || conda-env create -n CNAprioritization -f envs/pipeline.yaml &&
 source activate CNAprioritization &&
 snakemake --unlock &&
 ##Run snakemake
 snakemake -p \
-	--configfile /home/bftan/PrioritizationCNAs/config.yaml \
-	--snakefile /home/bftan/PrioritizationCNAs/Snakefile \
+	--configfile config.yaml \
+	--snakefile Snakefile \
 	--latency-wait 90 \
 	--jobs 1 \
 	--max-jobs-per-second 10 \
 	--restart-times 3 \
 	--use-conda \
-        --conda-prefix /home/bftan/.conda
+    --conda-prefix ~/.conda