Commit 35d2dcf8 authored by Beatrice Tan's avatar Beatrice Tan
parents 75205c4f 0c50f100
......@@ -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:
......
#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
......
......@@ -22,4 +22,4 @@ snakemake -p \
--max-jobs-per-second 10 \
--restart-times 3 \
--use-conda \
--conda-prefix ~/.conda
--conda-prefix ~/.conda
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