Add phasing window to beagle

genepi · Jun 14, 2024 · 6480436 · 6480436
1 parent 1874b47
commit 6480436
Showing 1 changed file with 5 additions and 2 deletions.
diff --git a/modules/local/phasing/beagle.nf b/modules/local/phasing/beagle.nf
@@ -14,14 +14,17 @@ process BEAGLE {
     // replace X.nonPAR etc with X for phasing
     def chr_cleaned = "${chr}".startsWith('X.') ? 'X' : "${chr}"
     def chr_mapped = "${params.refpanel.build}" == 'hg38' ? 'chr' + "${chr_cleaned}" : "${chr_cleaned}"
-
+    def phasing_start = "${start}".toInteger() - "${params.phasing_window}".toInteger()
+    phasing_start = "$phasing_start" < 0 ? 1 : "$phasing_start"
+    def phasing_end = "${end}".toInteger() + "${params.phasing_window}".toInteger()
+
     """
     java -jar /usr/bin/beagle.18May20.d20.jar \
         ref=${bcf}  \
         gt=${chunkfile} \
         out=${chunkfile_name}.phased \
         nthreads=${task.cpus} \
-        chrom=${chr_mapped}:${start}-${end} \
+        chrom=${chr_mapped}:${phasing_start}-${phasing_end} \
         map=${map_beagle} \
         impute=false 
     """