diff --git a/CHANGELOG.md b/CHANGELOG.md
index 38163a846fdec38f1b4d37fc3f007530b0c73414..b7b2b0d4fa24ff3882ac08272fb79901510bdc36 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,6 +11,7 @@ that users understand how the changes affect the new version.
 
 version 1.0.0-dev
 ---------------------------
++ All inputs to bedtools Sort are now reflected in the generated command
 + Add WDL task for TALON
 + Add WDL task for TranscriptClean
 + Fastqsplitter: fix mkdir command to work with biocontainer's busybox mkdir
diff --git a/bedtools.wdl b/bedtools.wdl
index 9ef29adf3ab9df067c78a8f0e6d485bcb4efecaf..f9859f93516503e4b4486a3e7ebab1129d42d943 100644
--- a/bedtools.wdl
+++ b/bedtools.wdl
@@ -30,7 +30,6 @@ task Sort {
         Boolean chrThenScoreD = false
         File? g
         File? faidx
-        Boolean header = false
         String outputBed = "output.sorted.bed"
         String dockerImage = "quay.io/biocontainers/bedtools:2.23.0--hdbcaa40_3"
     }
@@ -40,9 +39,11 @@ task Sort {
         mkdir -p $(dirname ~{outputBed})
         bedtools sort \
         -i ~{inputBed} \
-        ~{if sizeA then "-sizeA" else ""} \
-        ~{if sizeD then "-sizeD" else ""} \
-        ~{if chrThenSizeD then "-chrThenSizeD" else ""} \
+        ~{true="-sizeA" false="" sizeA} \
+        ~{true="-sizeD" false="" sizeD} \
+        ~{true="-chrThenScoreD" false="" chrThenScoreD} \
+        ~{"-g " + g} \
+        ~{"-faidx" + faidx} \
         > ~{outputBed}
     }
 
@@ -53,6 +54,4 @@ task Sort {
     runtime {
         docker: dockerImage
     }
-
-
-}
\ No newline at end of file
+}