Merge pull request #27 from icgc-argo/sanger-wgs-variant-caller.2.1.0-9

Sanger wgs variant caller.2.1.0 9
icgc-argo-workflows · May 13, 2020 · 0673480 · 0673480
2 parents e91d24f + 30811fe
commit 0673480
Showing 1 changed file with 7 additions and 5 deletions.
diff --git a/tools/sanger-wgs-variant-caller/sanger-wgs-variant-caller.nf b/tools/sanger-wgs-variant-caller/sanger-wgs-variant-caller.nf
@@ -23,7 +23,7 @@
  */
 
 nextflow.preview.dsl=2
-version = '2.1.0-6'
+version = '2.1.0-9'
 
 params.ref_genome_tar = ""
 params.vagrent_annot = ""
@@ -41,8 +41,8 @@ params.skipqc = false
 params.skipannot = false
 params.pindelcpu = 8
 params.cavereads = 350000
-params.purity = 1.0
-params.ploidy = 2.0
+params.purity = null
+params.ploidy = null
 params.container_version = ""
 params.cpus = 24
 params.mem = 128  // GB
@@ -86,6 +86,8 @@ process sangerWgsVariantCaller {
   script:
     arg_skipqc = params.skipqc ? "-skipqc" : ""
     arg_skipannot = params.skipannot ? "-skipannot" : ""
+    arg_pu = (params.purity!=null) ? "-pu ${params.purity}" : ""
+    arg_pi = (params.ploidy!=null) ? "-pi ${params.ploidy}" : ""
     """
     /opt/wtsi-cgp/bin/ds-cgpwgs.pl \
       -cores ${task.cpus} \
@@ -105,8 +107,8 @@ process sangerWgsVariantCaller {
       ${arg_skipannot} \
       -pindelcpu ${params.pindelcpu} \
       -cavereads ${params.cavereads} \
-      -pu ${params.purity} \
-      -pi ${params.ploidy} \
+      ${arg_pu} \
+      ${arg_pi} \
       -outdir \$PWD
     """
 }