diff --git a/cli/src/main/scala/org/bdgenomics/cannoli/cli/Bedtools.scala b/cli/src/main/scala/org/bdgenomics/cannoli/cli/Bedtools.scala
index b9dea64e..1e58ff1d 100644
--- a/cli/src/main/scala/org/bdgenomics/cannoli/cli/Bedtools.scala
+++ b/cli/src/main/scala/org/bdgenomics/cannoli/cli/Bedtools.scala
@@ -98,9 +98,9 @@ class BedtoolsFn(
       .setExecutable(args.executable)
       .add("intersect")
       .add("-a")
-      .add(optA.fold("stdin")(if (args.addFiles) "$0" else _))
+      .add(optA.fold("stdin")(f => if (args.addFiles) "$0" else absolute(f)))
       .add("-b")
-      .add(optB.fold("stdin")(if (args.addFiles) "$0" else _))
+      .add(optB.fold("stdin")(f => if (args.addFiles) "$0" else absolute(f)))
 
     if (args.sorted) builder.add("-sorted")
     if (args.addFiles) builder.addFile(file)
diff --git a/cli/src/main/scala/org/bdgenomics/cannoli/cli/Bowtie.scala b/cli/src/main/scala/org/bdgenomics/cannoli/cli/Bowtie.scala
index 6be7198b..bb894d32 100644
--- a/cli/src/main/scala/org/bdgenomics/cannoli/cli/Bowtie.scala
+++ b/cli/src/main/scala/org/bdgenomics/cannoli/cli/Bowtie.scala
@@ -74,7 +74,7 @@ class BowtieFn(
     val builder = CommandBuilders.create(args.useDocker, args.useSingularity)
       .setExecutable(args.executable)
       .add("-S")
-      .add(if (args.addFiles) "$0" else args.indexPath)
+      .add(if (args.addFiles) "$0" else absolute(args.indexPath))
       .add("--interleaved")
       .add("-")
 
diff --git a/cli/src/main/scala/org/bdgenomics/cannoli/cli/Bowtie2.scala b/cli/src/main/scala/org/bdgenomics/cannoli/cli/Bowtie2.scala
index a7ee6d9a..5079f11f 100644
--- a/cli/src/main/scala/org/bdgenomics/cannoli/cli/Bowtie2.scala
+++ b/cli/src/main/scala/org/bdgenomics/cannoli/cli/Bowtie2.scala
@@ -74,7 +74,7 @@ class Bowtie2Fn(
     val builder = CommandBuilders.create(args.useDocker, args.useSingularity)
       .setExecutable(args.executable)
       .add("-x")
-      .add(if (args.addFiles) "$0" else args.indexPath)
+      .add(if (args.addFiles) "$0" else absolute(args.indexPath))
       .add("--interleaved")
       .add("-")
 
diff --git a/cli/src/main/scala/org/bdgenomics/cannoli/cli/Freebayes.scala b/cli/src/main/scala/org/bdgenomics/cannoli/cli/Freebayes.scala
index d18c0506..c1e16dfe 100644
--- a/cli/src/main/scala/org/bdgenomics/cannoli/cli/Freebayes.scala
+++ b/cli/src/main/scala/org/bdgenomics/cannoli/cli/Freebayes.scala
@@ -83,7 +83,7 @@ class FreebayesFn(
     var builder = CommandBuilders.create(args.useDocker, args.useSingularity)
       .setExecutable(args.executable)
       .add("--fasta-reference")
-      .add(if (args.addFiles) "$0" else args.referencePath)
+      .add(if (args.addFiles) "$0" else absolute(args.referencePath))
       .add("--stdin")
       .add("--strict-vcf")
 
diff --git a/cli/src/main/scala/org/bdgenomics/cannoli/cli/Samtools.scala b/cli/src/main/scala/org/bdgenomics/cannoli/cli/Samtools.scala
index f123f949..60f23f6b 100644
--- a/cli/src/main/scala/org/bdgenomics/cannoli/cli/Samtools.scala
+++ b/cli/src/main/scala/org/bdgenomics/cannoli/cli/Samtools.scala
@@ -77,7 +77,7 @@ class SamtoolsFn(
       .add("mpileup")
       .add("-")
       .add("--reference")
-      .add(if (args.addFiles) "$0" else args.referencePath)
+      .add(if (args.addFiles) "$0" else absolute(args.referencePath))
       .add("-v")
       .add("-u")
 
diff --git a/cli/src/main/scala/org/bdgenomics/cannoli/cli/Vt.scala b/cli/src/main/scala/org/bdgenomics/cannoli/cli/Vt.scala
index 308744c5..5daa3837 100644
--- a/cli/src/main/scala/org/bdgenomics/cannoli/cli/Vt.scala
+++ b/cli/src/main/scala/org/bdgenomics/cannoli/cli/Vt.scala
@@ -82,7 +82,7 @@ class VtFn(
       .add("normalize")
       .add("-")
       .add("-r")
-      .add(if (args.addFiles) "$0" else args.referencePath)
+      .add(if (args.addFiles) "$0" else absolute(args.referencePath))
 
     Option(args.window).foreach(i => builder.add("-w").add(i.toString))