Commit 4a39be4b authored by Beatrice Tan's avatar Beatrice Tan

Updated settings and all input.

parent e1f63a7a
......@@ -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."""
......
......@@ -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",
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment