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Beatrice Tan
CNAprioritization
Commits
063e5890
Commit
063e5890
authored
Jan 31, 2018
by
BeatriceTan
Browse files
Merge branch 'master' of
https://gitlab.com/BeatriceTan/PrioritizationCNAs
parents
82ca2106
aebc3574
Changes
3
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Snakefile
View file @
063e5890
...
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@@ -42,8 +42,8 @@ onerror:
rule all:
"""Define desired output from pipeline."""
input:
#
"Samplesize/Report.txt",
"Reports/Tools.txt",
"Samplesize/Report.txt",
#
"Reports/Tools.txt",
#"Reports/Overlap_regions.bed"
#"Reports/Segments.txt",
#"GO/comparison.txt"
...
...
config.yaml
View file @
063e5890
#Directories to be specified
workdir
:
/home/bftan/CNA_results
#directory to write output
workdir
:
/home/bftan/CNA_results
2
#directory to write output
gisticdir
:
/home/bftan/Tools/GISTIC2
#directory to install GISTIC2
#workdir: /home/beatrice/CNA_analysis
...
...
@@ -31,6 +31,6 @@ settings_gistic: "-ta 0.1
-conf
0.99"
#Settings for sample size differences
#sizes: [
20,
30, 40, 50, 60, 70, 80, 90]
sizes
:
[
2
0
]
#sizes: [30, 40, 50, 60, 70, 80, 90]
sizes
:
[
30
,
4
0
]
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rules/GISTIC2.smk
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063e5890
...
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@@ -13,7 +13,8 @@ rule run_gistic:
gistic_directory=config["gisticdir"],
seg="Input/Segments_tumor.txt"
output:
"GISTIC/all_lesions.conf_" + config["gistic_precision"] + ".txt"
"GISTIC/all_lesions.conf_" + config["gistic_precision"] + ".txt",
"GISTIC/regions_track.conf_" + config["gistic_precision"] + ".bed"
params:
cnv="",
ref=config["reference"],
...
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