Merge pull request #81 from annahoge/patch-1

Patch 1
gavinha · Nov 7, 2019 · 97413f0 · 97413f0
2 parents b8cd44d + 3c0fcb4
commit 97413f0
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Showing 4 changed files with 15 additions and 11 deletions.
diff --git a/scripts/snakemake/TitanCNA.snakefile b/scripts/snakemake/TitanCNA.snakefile
@@ -112,9 +112,9 @@ rule copyOptSolution:
 		curDir=`pwd`
 		for i in `cut -f11 {input} | grep -v "path"`;
 		do
-			echo -e "Creating sym links for $curDir/${{i}} to {output}"
-			ln -s ${{curDir}}/${{i}}* {output}
+			echo -e "Copying $curDir/${{i}} to {output}"
+			cp ${{curDir}}/${{i}}* {output}
 		done		
 		"""
 
-
+
diff --git a/scripts/snakemake/config/config.yaml b/scripts/snakemake/config/config.yaml
@@ -1,5 +1,6 @@
 ## path to tools
 samTools:  /path/to/samtools
+bcfTools:  /path/to/bcftools
 
 ## path to scripts ##
 readCounterScript:  /path/to/readCounter

diff --git a/scripts/snakemake/getAlleleCounts.snakefile b/scripts/snakemake/getAlleleCounts.snakefile
@@ -21,11 +21,12 @@ rule getHETsites:
 	params:
 		refFasta=config["refFasta"],
 		snpDB=config["snpVCF"],
-		samtoolsCmd=config["samTools"]
+		samtoolsCmd=config["samTools"],
+		bcftoolsCmd=config["bcfTools"]
 	log:
 		"logs/titan/hetPosns/{tumor}/{tumor}.chr{chr}.log"
 	shell:
-		"{params.samtoolsCmd} mpileup -uv -I -f {params.refFasta} -r {wildcards.chr} -l {params.snpDB} {input} | bcftools call -v -c - | grep -e '0/1' -e '#' > {output} 2> {log}"
+		"{params.samtoolsCmd} mpileup -uv -I -f {params.refFasta} -r {wildcards.chr} -l {params.snpDB} {input} | {params.bcftoolsCmd} call -v -c - | grep -e '0/1' -e '#' > {output} 2> {log}"
 
 
 rule getAlleleCountsByChr:

diff --git a/scripts/snakemake/ichorCNA.snakefile b/scripts/snakemake/ichorCNA.snakefile
@@ -2,10 +2,12 @@ configfile: "config/config.yaml"
 configfile: "config/samples.yaml"
 
 rule correctDepth:
-  input: 
-  	expand("results/ichorCNA/{tumor}/{tumor}.cna.seg", tumor=config["pairings"]),
-  	expand("results/ichorCNA/{tumor}/{tumor}.correctedDepth.txt", tumor=config["pairings"]),
-  	expand("results/readDepth/{samples}.bin{binSize}.wig", samples=config["samples"], binSize=str(config["binSize"]))
+	input:
+		expand("results/ichorCNA/{tumor}/{tumor}.cna.seg", tumor=config["pairings"]),
+		expand("results/ichorCNA/{tumor}/{tumor}.seg.txt", tumor=config["pairings"]),
+		expand("results/ichorCNA/{tumor}/{tumor}.params.txt", tumor=config["pairings"]),
+		expand("results/ichorCNA/{tumor}/{tumor}.correctedDepth.txt", tumor=config["pairings"]),
+		expand("results/readDepth/{samples}.bin{binSize}.wig", samples=config["samples"], binSize=str(config["binSize"]))
 
 rule read_counter:
 	input:
@@ -30,9 +32,9 @@ rule ichorCNA:
 		norm=lambda wildcards: "results/readDepth/" + config["pairings"][wildcards.tumor] + ".bin" + str(config["binSize"]) + ".wig"
 	output:
 		corrDepth="results/ichorCNA/{tumor}/{tumor}.correctedDepth.txt",
-		#param="results/ichorCNA/{tumor}/{tumor}.params.txt",
+		param="results/ichorCNA/{tumor}/{tumor}.params.txt",
 		cna="results/ichorCNA/{tumor}/{tumor}.cna.seg",
-		#segTxt="results/ichorCNA/{tumor}/{tumor}.seg.txt",
+		segTxt="results/ichorCNA/{tumor}/{tumor}.seg.txt",
 		#seg="results/ichorCNA/{tumor}/{tumor}.seg",
 		#rdata="results/ichorCNA/{tumor}/{tumor}.RData",
 	params: