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Beatrice Tan
CNAprioritization
Commits
153ad922
Commit
153ad922
authored
Feb 19, 2018
by
Beatrice Tan
Browse files
Updated settings.
parent
8ffa81e4
Changes
2
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Snakefile
View file @
153ad922
...
...
@@ -18,7 +18,6 @@ include: "rules/GenePrioritization.smk"
include: "rules/ComparisonRegions.smk"
include: "rules/Circos.smk"
include: "rules/SampleSizes.smk"
#include: "rules/UseControl.smk"
include: "rules/ComparisonSettings.smk"
#Directory to save all files.
...
...
@@ -45,8 +44,9 @@ rule all:
"""Define desired output from pipeline."""
input:
#"Settings/Report.txt",
"PipelineResults.html",
"ComparisonResults.html"
"Samplesize/Report.txt"
#"PipelineResults.html",
#"GO/comparison.txt",
rule help:
"""Print list of all targets with help."""
...
...
config.yaml
View file @
153ad922
...
...
@@ -2,7 +2,7 @@
#workdir: /home/bftan/CNA_results #directory to write output
#gisticdir: /home/bftan/Tools/GISTIC2 #directory to install GISTIC2
workdir
:
/home/beatrice/CNA_99_genegistic
workdir
:
/home/beatrice/CNA_
analysis
#CNA_
99_genegistic
gisticdir
:
/home/beatrice/CNA_analysis/run_gistic2
#Input details to download from firehose
...
...
@@ -32,5 +32,5 @@ comparison_settings: ["-brlen 0.7 -genegistic 1",
"
-brlen
0.7
-genegistic
0"
]
#Settings for sample size differences
sizes
:
[
20
,
30
,
40
,
50
,
60
,
70
,
80
,
90
,
100
,
110
]
sizes
:
[
20
,
30
,
40
,
50
,
60
,
70
,
80
,
90
]
repeats
:
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]
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