Commit 3e2c380f authored by Tan's avatar Tan
Browse files

Updated run rule for running different sample sizes with GISTIC2.

parent 0c50f100
...@@ -42,7 +42,7 @@ onerror: ...@@ -42,7 +42,7 @@ onerror:
rule all: rule all:
"""Define desired output from pipeline.""" """Define desired output from pipeline."""
input: input:
os.path.join(config["gisticdir"], "gistic2") "Samplesize/Report.txt"
#"Reports/Results.html" #"Reports/Results.html"
......
...@@ -34,6 +34,6 @@ settings_gistic: "-ta 0.1 ...@@ -34,6 +34,6 @@ settings_gistic: "-ta 0.1
-conf 0.99" -conf 0.99"
#Settings for sample size differences #Settings for sample size differences
#sizes: [30, 40, 50, 60, 70, 80, 90] sizes: [20, 30, 40, 50, 60, 70, 80, 90]
sizes: [30, 40] #sizes: [30, 40]
repeats: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] repeats: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20]
...@@ -18,9 +18,9 @@ rule run_gistic_subsets: ...@@ -18,9 +18,9 @@ rule run_gistic_subsets:
seg="Samplesize/Input/Size{rand_nr}.Rep{rep_nr}.txt" seg="Samplesize/Input/Size{rand_nr}.Rep{rep_nr}.txt"
output: output:
"Samplesize/GISTIC/Size{rand_nr}.Rep{rep_nr}/all_lesions.conf_" + config["gistic_precision"] + ".txt" "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: params:
cnv="", cnv="",
gistic_directory=config["gisticdir"],
ref=config["reference"], ref=config["reference"],
ref_file="", ref_file="",
extra=config["settings_gistic"] extra=config["settings_gistic"]
...@@ -50,7 +50,7 @@ rule run_rubic_subsets: ...@@ -50,7 +50,7 @@ rule run_rubic_subsets:
rule report_sizes: rule report_sizes:
"""Report the difference when using different sample sizes.""" """Report the difference when using different sample sizes."""
input: 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_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"]) rubic_losses=expand("Samplesize/RUBIC/Size{rand_nr}.Rep{rep_nr}/losses.txt", rand_nr=config["sizes"], rep_nr=config["repeats"])
output: output:
......
...@@ -18,7 +18,7 @@ snakemake -p \ ...@@ -18,7 +18,7 @@ snakemake -p \
--configfile config.yaml \ --configfile config.yaml \
--snakefile Snakefile \ --snakefile Snakefile \
--latency-wait 90 \ --latency-wait 90 \
--jobs 1 \ --jobs 3 \
--max-jobs-per-second 10 \ --max-jobs-per-second 10 \
--restart-times 3 \ --restart-times 3 \
--use-conda \ --use-conda \
......
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