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CNAprioritization
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Beatrice Tan
CNAprioritization
Commits
35d2dcf8
Commit
35d2dcf8
authored
Feb 02, 2018
by
Beatrice Tan
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Merge branch 'master' of
https://git.lumc.nl/bftan/CNAprioritization
parents
75205c4f
0c50f100
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3
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Snakefile
Snakefile
+3
-2
config.yaml
config.yaml
+5
-2
run_pipeline_cluster.sh
run_pipeline_cluster.sh
+1
-1
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Snakefile
View file @
35d2dcf8
...
...
@@ -4,7 +4,7 @@ configfile: "config.yaml"
#Add directory with scripts to the Python path
import sys
sys.path.insert(0, workflow.basedir + "/scripts")
import os.path
#Rules to run pipeline for prioritization of regions and genes.
include: "rules/PreprocessInput.smk"
...
...
@@ -42,7 +42,8 @@ onerror:
rule all:
"""Define desired output from pipeline."""
input:
"Reports/Results.html"
os.path.join(config["gisticdir"], "gistic2")
#"Reports/Results.html"
rule help:
...
...
config.yaml
View file @
35d2dcf8
#Directories to be specified
workdir
:
/home/bftan/CNA_results
#directory to write output
gisticdir
:
/home/bftan/Tools/GISTIC2_test
#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
...
...
run_pipeline_cluster.sh
View file @
35d2dcf8
...
...
@@ -22,4 +22,4 @@ snakemake -p \
--max-jobs-per-second
10
\
--restart-times
3
\
--use-conda
\
--conda-prefix
~/.conda
--conda-prefix
~/.conda
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