Commit 153ad922 authored by Beatrice Tan's avatar Beatrice Tan

Updated settings.

parent 8ffa81e4
......@@ -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."""
......
......@@ -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: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20]
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