Make subsampling seed input optional

Author: kjaisingh

src/WGD/bin/medianCoverage.R

@@ -19,7 +19,7 @@ option_list <- list(
               help="compute median absolute deviation of all bins per sample [default: FALSE]"),
   make_option(c("-H","--header"), action="store_true", default=FALSE,
               help="input coverage matrix has header with sample IDs [default: FALSE]"),
-  make_option(c("-s","--seed"), type="integer", default=NULL,
+  make_option(c("-s","--seed"), type="integer", default=42,
               help="random seed for reproducible sampling [default: no seed set]"))
 
 # Get command-line arguments and options
@@ -28,10 +28,8 @@ args <- parse_args(OptionParser(usage="%prog [options] covMatrix.bed OUTFILE",
                    positional_arguments=TRUE)
 opts <- args$options
 
-# Set random seed if provided
-if(!is.null(opts$seed)){
-  set.seed(opts$seed)
-}
+# Set random seed
+set.seed(opts$seed)
 
 # Checks for appropriate positional arguments
 if(length(args$args) != 2)

wdl/MedianCov.wdl

@@ -11,7 +11,7 @@ workflow MedianCov {
     Float? mem_gb_override
     String sv_pipeline_qc_docker
     RuntimeAttr? runtime_attr
-    Int? subsample_seed = 42
+    Int? subsample_seed
   }
 
   call CalcMedCov {
@@ -33,7 +33,7 @@ task CalcMedCov {
   input {
     File bincov_matrix
     String cohort_id
-    Int sesubsample_seeded
+    Int? subsample_seed
     Float? mem_gb_override
     String sv_pipeline_qc_docker
     RuntimeAttr? runtime_attr_override
@@ -56,7 +56,11 @@ task CalcMedCov {
 
     set -euo pipefail
     zcat ~{bincov_matrix} > ~{cohort_id}_fixed.bed 
-    Rscript /opt/WGD/bin/medianCoverage.R ~{cohort_id}_fixed.bed -H --seed ~{subsample_seed} ~{cohort_id}_medianCov.bed
+    Rscript /opt/WGD/bin/medianCoverage.R \
+      ~{cohort_id}_fixed.bed \
+      -H \
+      ~{if defined(subsample_seed) then "--seed ~{subsample_seed}" else ""}
+      ~{cohort_id}_medianCov.bed
     Rscript -e "x <- read.table(\"~{cohort_id}_medianCov.bed\",check.names=FALSE); xtransposed <- t(x[,c(1,2)]); write.table(xtransposed,file=\"~{cohort_id}_medianCov.transposed.bed\",sep=\"\\t\",row.names=F,col.names=F,quote=F)"
   
   >>>