Fix far command for GSAlign

MazdaX · Dec 7, 2020 · b3bee3a · b3bee3a
1 parent 61f59b2
commit b3bee3a
Showing 1 changed file with 1 addition and 0 deletions.
diff --git a/modules/processes/GSAlign.nf b/modules/processes/GSAlign.nf
@@ -105,6 +105,7 @@ process gsalign_far{
 
     script:
     """
+    GSAlign -i ${srcname} -q ${tgtfile} -t ${task.cpus} -idy 75 -no_vcf -o ${srcname}.${tgtname}.tmp
     if [ -e ${srcname}.${tgtname}.tmp.maf ]; then
         sed 's/ref.//g' ${srcname}.${tgtname}.tmp.maf | 
             sed 's/qry.//g' |