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CNAprioritization
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Beatrice Tan
CNAprioritization
Commits
0c65624f
Commit
0c65624f
authored
Feb 03, 2018
by
Tan
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Updated sample size test.
parent
3e2c380f
Changes
4
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4 changed files
with
9 additions
and
9 deletions
+9
-9
config.yaml
config.yaml
+1
-1
rules/SampleSizes.smk
rules/SampleSizes.smk
+4
-3
run_pipeline_cluster.sh
run_pipeline_cluster.sh
+4
-4
wrappers/GISTIC2/environment.yaml
wrappers/GISTIC2/environment.yaml
+0
-1
No files found.
config.yaml
View file @
0c65624f
#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
...
...
rules/SampleSizes.smk
View file @
0c65624f
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="",
...
...
run_pipeline_cluster.sh
View file @
0c65624f
...
...
@@ -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
wrappers/GISTIC2/environment.yaml
View file @
0c65624f
channels
:
-
bioconda
-
conda-forge
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