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Beatrice Tan
CNAprioritization
Commits
4a39be4b
Commit
4a39be4b
authored
Feb 07, 2018
by
Beatrice Tan
Browse files
Updated settings and all input.
parent
e1f63a7a
Changes
2
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Snakefile
View file @
4a39be4b
...
...
@@ -17,6 +17,7 @@ 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.
workdir: config["workdir"]
...
...
@@ -42,11 +43,13 @@ onerror:
rule all:
"""Define desired output from pipeline."""
input:
"Settings/Report.txt",
#"Samplesize/Precision_recall.png"
#"Reports/Overlap_plots/NUP107.png"
#"Settings/Report.txt",
#"Samplesize/Report.txt",
#"Reports/Tools.txt",
"Reports/Tools.txt",
"Reports/Circos/RecurrentRegions.png",
"GO/comparison.txt"
# "Samplesize/Report.txt"
rule help:
"""Print list of all targets with help."""
...
...
config.yaml
View file @
4a39be4b
...
...
@@ -25,14 +25,7 @@ ID_to_GO: input_files/ID_to_GO.txt
#Settings GISTIC2.0
gistic_precision
:
"
99"
settings_gistic
:
"
-ta
0.1
-td
0.1
-qvt
0.25
-brlen
0.7
-cap
1.5
-rx
1
-genegistic
1
-conf
0.99"
settings_gistic
:
"
"
comparison_settings
:
[
"
-ta
0.1
-td
0.1
-qvt
0.25
-brlen
0.7
-cap
1.5
-rx
1
-genegistic
1
-conf
0.99"
,
"
-ta
0.1
-td
0.1
-qvt
0.25
-brlen
0.7
-cap
1.5
-rx
1
-genegistic
1
-conf
0.75"
,
...
...
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