Updated run rule for running different sample sizes with GISTIC2.

Snakefile

@@ -42,7 +42,7 @@ onerror:
 rule all:
     """Define desired output from pipeline."""
     input:
-        os.path.join(config["gisticdir"], "gistic2")
+        "Samplesize/Report.txt"
         #"Reports/Results.html"
 
 

config.yaml

@@ -34,6 +34,6 @@ settings_gistic: "-ta 0.1
                   -conf 0.99"
 
 #Settings for sample size differences
-#sizes: [30, 40, 50, 60, 70, 80, 90]
-sizes: [30, 40]
+sizes: [20, 30, 40, 50, 60, 70, 80, 90]
+#sizes: [30, 40]
 repeats: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20]

rules/SampleSizes.smk

@@ -18,9 +18,9 @@ rule run_gistic_subsets:
         seg="Samplesize/Input/Size{rand_nr}.Rep{rep_nr}.txt"
     output:
         "Samplesize/GISTIC/Size{rand_nr}.Rep{rep_nr}/all_lesions.conf_" + config["gistic_precision"] + ".txt"
+        "Samplesize/GISTIC/Size{rand_nr}.Rep{rep_nr}/regions_track.conf_" + config["gistic_precision"] + ".bed"
     params:
         cnv="",
-        gistic_directory=config["gisticdir"],
         ref=config["reference"],
         ref_file="",
         extra=config["settings_gistic"]
@@ -50,7 +50,7 @@ rule run_rubic_subsets:
 rule report_sizes:
     """Report the difference when using different sample sizes."""
     input:
-        #gistic=expand("Samplesize/GISTIC/Size{rand_nr}.Rep{rep_nr}/all_lesions.conf_" + config["gistic_precision"] + ".txt", rand_nr=config["sizes"], rep_nr=config["repeats"]),
+        gistic=expand("Samplesize/GISTIC/Size{rand_nr}.Rep{rep_nr}/all_lesions.conf_" + config["gistic_precision"] + ".txt", rand_nr=config["sizes"], rep_nr=config["repeats"]),
         rubic_gains=expand("Samplesize/RUBIC/Size{rand_nr}.Rep{rep_nr}/gains.txt", rand_nr=config["sizes"], rep_nr=config["repeats"]),
         rubic_losses=expand("Samplesize/RUBIC/Size{rand_nr}.Rep{rep_nr}/losses.txt", rand_nr=config["sizes"], rep_nr=config["repeats"])
     output:

run_pipeline_cluster.sh

@@ -18,7 +18,7 @@ snakemake -p \
 	--configfile config.yaml \
 	--snakefile Snakefile \
 	--latency-wait 90 \
-	--jobs 1 \
+	--jobs 3 \
 	--max-jobs-per-second 10 \
 	--restart-times 3 \
 	--use-conda \