Added a chr- function for readCounter

modules/ichorcna/1.0/config/default.yaml

@@ -12,12 +12,6 @@ lcr-modules:
 
         options:
             readcounter:
-                chrs:
-                    hg19: "1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y"
-                    grch37: "1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y"
-                    hs37d5: "1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y"
-                    hg38: "chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX,chrY"
-                    grch38: "chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX,chrY"
                 qual: 20 # only includes reads with mapping quality greater than 20
                 binSize:  1000000 # set window size to compute coverage 
                 # available binSizes are: 1000000, 500000, 50000, 10000

modules/ichorcna/1.0/ichorcna.smk

@@ -182,6 +182,17 @@ rule _ichorcna_input_bam:
         op.absolute_symlink(input.bam, output.bam)
         op.absolute_symlink(input.bai, output.bai)
 
+# This function will return a comma-separated list of chromosomes to include in readCounter
+def get_chromosomes(wildcards):
+    chromosomes=[]
+    for i in range(1,23):
+        chromosomes.append(str(i))
+    chromosomes.append("X")
+    chromosomes.append("Y")
+    if "38" in str(wildcards.genome_build):
+        chromosomes = ["chr" + x for x in chromosomes]
+    chromosomes= ",".join(chromosomes)    
+    return chromosomes
 
 rule _ichorcna_read_counter:
     input:
@@ -194,7 +205,7 @@ rule _ichorcna_read_counter:
     params:
         binSize = CFG["options"]["readcounter"]["binSize"],
         qual = CFG["options"]["readcounter"]["qual"],
-        chrs = op.switch_on_wildcard("genome_build", CFG["options"]["readcounter"]["chrs"])
+        chrs = get_chromosomes
     conda: CFG["conda_envs"]["ichorcna"]
     threads: CFG["threads"]["readcounter"]
     resources: