Merge branch 'master' of https://git.lumc.nl/bftan/CNAprioritization

Snakefile

@@ -4,7 +4,7 @@ configfile: "config.yaml"
 #Add directory with scripts to the Python path
 import sys
 sys.path.insert(0, workflow.basedir + "/scripts")
-
+import os.path
 
 #Rules to run pipeline for prioritization of regions and genes.
 include: "rules/PreprocessInput.smk"
@@ -42,7 +42,8 @@ onerror:
 rule all:
     """Define desired output from pipeline."""
     input:
-        "Reports/Results.html"
+        os.path.join(config["gisticdir"], "gistic2")
+        #"Reports/Results.html"
 
 
 rule help:

config.yaml

 #Directories to be specified
+workdir: /home/bftan/CNA_results        #directory to write output
+gisticdir: /home/bftan/Tools/GISTIC2_test    #directory to install GISTIC2
+
 #workdir: /home/bftan/CNA_results        #directory to write output
 #gisticdir: /home/bftan/Tools/GISTIC2    #directory to install GISTIC2
 
-workdir: /home/beatrice/CNA_analysis
-gisticdir: /home/beatrice/CNA_analysis/run_gistic2
+#workdir: /home/beatrice/CNA_analysis
+#gisticdir: /home/beatrice/CNA_analysis/run_gistic2
 
 #Input details to download from firehose
 cancer_type: SKCM

run_pipeline_cluster.sh

@@ -22,4 +22,4 @@ snakemake -p \
 	--max-jobs-per-second 10 \
 	--restart-times 3 \
 	--use-conda \
-    --conda-prefix ~/.conda
+	--conda-prefix ~/.conda