Parallel mode of StrandPhaseR

Snakefile

@@ -304,6 +304,7 @@ rule run_strandphaser:
         "strand_states/" + config["sample"] + ".strandphaser_output.txt"
     log:
         "log/run_strandphaser.txt"
+    threads: 8
     shell:
         """
         Rscript utils/StrandPhaseR_pipeline.R \
@@ -313,6 +314,7 @@ rule run_strandphaser:
                 {input.wcregions} \
                 {input.snppositions} \
                 $(pwd)/utils/R-packages/ \
+                {threads} \
                 > {log} 2>&1
         cp log/StrandPhaseR_analysis/Phased/phased_haps.txt {output}
         """

utils/StrandPhaseR_pipeline.R

@@ -8,4 +8,4 @@ args=commandArgs(TRUE)
 suppressPackageStartupMessages(library(StrandPhaseR))
 suppressPackageStartupMessages(library(BSgenome.Hsapiens.UCSC.hg19))
 
-strandPhaseR(inputfolder=args[1], outputfolder=args[2], configfile = args[3],  WCregions = args[4] , positions=args[5])
+strandPhaseR(inputfolder=args[1], outputfolder=args[2], configfile = args[3],  WCregions = args[4] , positions=args[5], numCPU=args[7])