Use absolute path when not using -add_files.

bigdatagenomics · Mar 21, 2018 · b8c3c0b · b8c3c0b
1 parent e636667
commit b8c3c0b
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Showing 6 changed files with 7 additions and 7 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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))