Commit 3e3420b4 authored by Beatrice Tan's avatar Beatrice Tan

Improved config file and updated workdir in rules.

parent 963296f4
from os.path import join
configfile: "config.yaml"
include: "rules/recurrent_regions.smk"
......@@ -12,9 +10,9 @@ include: "rules/gene_prioritization.smk"
workdir: config["workdir"]
onstart:
shell("echo Initiating pipeline to identify recurrent CNAs and relevant genes from tumor copy number profiles.")
shell("echo Executing pipeline to identify recurrent CNAs and candidate genes from tumor copy number profiles.")
shell("echo - Inputfile: " + config["inputfile"])
shell("echo - Snakefile, rules and wrappers in: {workflow.basedir}")
shell("echo - Snakefile, rules and wrappers directory: {workflow.basedir}")
shell("echo - Output directory: " + config["workdir"])
rule all:
......
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]
inputfile:
/home/beatrice/Documents/SASC/SKCM_segmentedCNAs/SKCM.cna__illuminahiseq_dnaseqc__hms_harvard_edu__Level_3__segmentation__seg.seg.txt
reference:
hg19
wkdir:
/home/beatrice/Documents/SASC
workdir:
/home/beatrice/Documents/SASC
gsdir:
/home/beatrice/Documents/SASC/run_GISTIC2
markerfile:
/home/beatrice/Documents/SASC/Input_files/markers.tsv
Prev_found_genes:
/home/beatrice/Documents/SASC/Input_files/intogen-CM-drivers-data.tsv
#/home/beatrice/Documents/SASC/Input_files/SKCM_genes.txt
Census_genes:
/home/beatrice/Documents/SASC/Input_files/Census_genes.txt
#Directories to be specified
workdir: /home/beatrice/Documents/SASC
gsdir: /home/beatrice/Documents/SASC/run_GISTIC2
#Input specifications
inputfile: /home/beatrice/Documents/SASC/SKCM_segmentedCNAs/SKCM.cna__illuminahiseq_dnaseqc__hms_harvard_edu__Level_3__segmentation__seg.seg.txt
reference: hg19
markerfile: /home/beatrice/Documents/SASC/Input_files/markers.tsv
Prev_found_genes: /home/beatrice/Documents/SASC/Input_files/intogen-CM-drivers-data.tsv #/home/beatrice/Documents/SASC/Input_files/SKCM_genes.txt
Census_genes: /home/beatrice/Documents/SASC/Input_files/Census_genes.txt
#Settings for sample size differences
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]
......@@ -27,7 +27,7 @@ rule run_gistic_random_subsets:
rule report_sizes:
input:
expand(join(config["wkdir"], "GISTIC_results", "{rand_nr}x{rep_nr}"), rand_nr=config["sizes"], rep_nr=config["repeats"])
expand(os.path.join("Recurrent/GISTIC2", "{rand_nr}x{rep_nr}"), rand_nr=config["sizes"], rep_nr=config["repeats"])
params:
census=config["Census_genes"],
known=config["Prev_found_genes"],
......
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