Commit 0c65624f authored by Tan's avatar Tan

Updated sample size test.

parent 3e2c380f
#Directories to be specified
workdir: /home/bftan/CNA_results #directory to write output
gisticdir: /home/bftan/Tools/GISTIC2_test #directory to install GISTIC2
gisticdir: /home/bftan/Tools/GISTIC2 #directory to install GISTIC2
#workdir: /home/bftan/CNA_results #directory to write output
#gisticdir: /home/bftan/Tools/GISTIC2 #directory to install GISTIC2
......
import ReportSizes
from SampleSizes import SegFile
from Rubic import MarkerFile
import os.path
import datetime
rule seg_subsets:
"""Create segmentation files with different numbers of samples (randomly chosen) for a number of times."""
......@@ -14,10 +15,10 @@ rule seg_subsets:
rule run_gistic_subsets:
"""Run GISTIC2 for the segmentation files with different subsets."""
input:
gistic_directory=config["gisticdir"],
gistic_directory=os.path.join(config["gisticdir"], "gistic2"),
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}/all_lesions.conf_" + config["gistic_precision"] + ".txt",
"Samplesize/GISTIC/Size{rand_nr}.Rep{rep_nr}/regions_track.conf_" + config["gistic_precision"] + ".bed"
params:
cnv="",
......
......@@ -18,8 +18,8 @@ snakemake -p \
--configfile config.yaml \
--snakefile Snakefile \
--latency-wait 90 \
--jobs 3 \
--jobs 1 \
--max-jobs-per-second 10 \
--restart-times 3 \
--use-conda \
--conda-prefix ~/.conda
--restart-times 3
# --use-conda \
# --conda-prefix ~/.conda
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