diff --git a/bin/convertAlleleCounts.r b/bin/convertAlleleCounts.r
index ee1ab2551e..284e879adf 100755
--- a/bin/convertAlleleCounts.r
+++ b/bin/convertAlleleCounts.r
@@ -1,4 +1,5 @@
-#!/bin/env Rscript
+#!/usr/bin/env Rscript
+
 # Description:
 # R-script for converting output from AlleleCount to BAF and LogR values.
 #
diff --git a/bin/run_ascat.r b/bin/run_ascat.r
index cdf6a65d14..d8800f91b2 100755
--- a/bin/run_ascat.r
+++ b/bin/run_ascat.r
@@ -1,4 +1,4 @@
-q#!/bin/env Rscript
+#!/usr/bin/env Rscript
 library("optparse")
 option_list = list(
     make_option("--tumorbaf", type="character", default=NULL,
diff --git a/main.nf b/main.nf
index 6f8f2ecd1e..1514395248 100644
--- a/main.nf
+++ b/main.nf
@@ -2569,7 +2569,7 @@ process ConvertAlleleCounts {
     script:
     gender = genderMap[idPatient]
     """
-    Rscript ${workflow.projectDir}/bin/convertAlleleCounts.r ${idSampleTumor} ${alleleCountTumor} ${idSampleNormal} ${alleleCountNormal} ${gender}
+    convertAlleleCounts.r ${idSampleTumor} ${alleleCountTumor} ${idSampleNormal} ${alleleCountNormal} ${gender}
     """
 }
 
@@ -2599,16 +2599,14 @@ process Ascat {
     ascat_ploidy=params.ascat_ploidy
     if (params.ascat_purity && params.ascat_ploidy)
     """
-        for f in *BAF *LogR; do sed 's/chr//g' \$f > tmpFile; mv tmpFile \$f;done
-        Rscript ${workflow.projectDir}/bin/run_ascat.r --tumorbaf ${bafTumor} --tumorlogr ${logrTumor} --normalbaf ${bafNormal} --normallogr ${logrNormal} --tumorname ${idSampleTumor} --basedir ${baseDir} --gcfile ${acLociGC} --gender ${gender} --purity ${ascat_purity} --ploidy ${ascat_ploidy}
+    for f in *BAF *LogR; do sed 's/chr//g' \$f > tmpFile; mv tmpFile \$f;done
+    run_ascat.r --tumorbaf ${bafTumor} --tumorlogr ${logrTumor} --normalbaf ${bafNormal} --normallogr ${logrNormal} --tumorname ${idSampleTumor} --basedir ${baseDir} --gcfile ${acLociGC} --gender ${gender} --purity ${ascat_purity} --ploidy ${ascat_ploidy}
     """
     else
     """
-        for f in *BAF *LogR; do sed 's/chr//g' \$f > tmpFile; mv tmpFile \$f;done
-        Rscript ${workflow.projectDir}/bin/run_ascat.r --tumorbaf ${bafTumor} --tumorlogr ${logrTumor} --normalbaf ${bafNormal} --normallogr ${logrNormal} --tumorname ${idSampleTumor} --basedir ${baseDir} --gcfile ${acLociGC} --gender ${gender}
+    for f in *BAF *LogR; do sed 's/chr//g' \$f > tmpFile; mv tmpFile \$f;done
+    run_ascat.r --tumorbaf ${bafTumor} --tumorlogr ${logrTumor} --normalbaf ${bafNormal} --normallogr ${logrNormal} --tumorname ${idSampleTumor} --basedir ${baseDir} --gcfile ${acLociGC} --gender ${gender}
     """
-
-
 }
 
 ascatOut.dump(tag:'ASCAT')