Commit c246d616 authored by Tan's avatar Tan

Removed errors.

parent ddbe27d0
......@@ -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 +43,11 @@ onerror:
rule all:
"""Define desired output from pipeline."""
input:
"GO/comparison.txt",
"Settings/Report.txt",
#"Samplesize/Report.txt",
#"Reports/Tools.txt",
"GO/comparison.txt"
# "Samplesize/Report.txt"
#"Samplesize/Report.txt"
rule help:
"""Print list of all targets with help."""
......
#Directories to be specified
#workdir: /home/bftan/CNA_results #directory to write output
#gisticdir: /home/bftan/Tools/GISTIC2 #directory to install GISTIC2
workdir: /home/bftan/CNA_results #directory to write output
gisticdir: /home/bftan/Tools/GISTIC2 #directory to install GISTIC2
#workdir: /home/bftan/CNA_results #directory to write output
#gisticdir: /home/bftan/Tools/GISTIC2 #directory to install GISTIC2
workdir: /home/beatrice/CNA_analysis
gisticdir: /home/beatrice/CNA_analysis/run_gistic2
#workdir: /home/beatrice/CNA_analysis
#gisticdir: /home/beatrice/CNA_analysis/run_gistic2
#Input details to download from firehose
cancer_type: SKCM
......
import os.path
rule gistic_settings:
"""Run GISTIC2 based on different settings."""
input:
gistic_directory=os.path.join(config["gisticdir"], "gistic2"),
seg="Input/Segments_tumor.txt"
output:
expand("Settings/GISTIC_{setting_nr}/all_lesions.conf_" + config["gistic_precision"] + ".txt", setting_nr=range(len(config["comparison_settings"])),
expand("Settings/GISTIC_{setting_nr}/regions_track.conf_" + config["gistic_precision"] + ".bed", setting_nr=range(len(config["comparison_settings"]))
expand("Settings/GISTIC_{setting_nr}/all_lesions.conf_" + config["gistic_precision"] + ".txt", setting_nr=range(len(config["comparison_settings"]))),
expand("Settings/GISTIC_{setting_nr}/regions_track.conf_" + config["gistic_precision"] + ".bed", setting_nr=range(len(config["comparison_settings"])))
params:
cnv="",
ref=config["reference"],
ref_file="",
extra=config["comparison_settings"][{setting_nr}]
extra=expand("{setting}", setting=config["comparison_settings"])
wrapper:
"file:" + workflow.basedir + "/wrappers/GISTIC2"
......
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