style fixes

centrifuge.wdl

@@ -120,7 +120,7 @@ task Classify {
 }
 
 task Download {
-        input {
+    input {
         String libraryPath
         Array[String]? domain
         String? executable = "centrifuge-download"

fastqc.wdl

@@ -24,27 +24,27 @@ task fastqc {
     # This regex chops of the extension and replaces it with _fastqc for the reportdir.
     # Just as fastqc does it.
     String reportDir = outdirPath + "/" + sub(basename(name), "\\.[^\\.]*$", "_fastqc")
-    command {
-    set -e -o pipefail
-    ~{preCommand}
-    mkdir -p ~{outdirPath}
-    fastqc \
-    ~{"--outdir " + outdirPath} \
-    ~{true="--casava" false="" casava} \
-    ~{true="--nano" false="" nano} \
-    ~{true="--nofilter" false="" noFilter} \
-    ~{true="--extract" false="" extract} \
-    ~{true="--nogroup" false="" nogroup} \
-    ~{"--min_length " + minLength } \
-    ~{"--format " + format} \
-    ~{"--threads " + threads} \
-    ~{"--contaminants " + contaminants} \
-    ~{"--adapters " + adapters} \
-    ~{"--limits " + limits} \
-    ~{"--kmers " + kmers} \
-    ~{"--dir " + dir} \
-    ~{seqFile}
 
+    command {
+        set -e -o pipefail
+        ~{preCommand}
+        mkdir -p ~{outdirPath}
+        fastqc \
+        ~{"--outdir " + outdirPath} \
+        ~{true="--casava" false="" casava} \
+        ~{true="--nano" false="" nano} \
+        ~{true="--nofilter" false="" noFilter} \
+        ~{true="--extract" false="" extract} \
+        ~{true="--nogroup" false="" nogroup} \
+        ~{"--min_length " + minLength } \
+        ~{"--format " + format} \
+        ~{"--threads " + threads} \
+        ~{"--contaminants " + contaminants} \
+        ~{"--adapters " + adapters} \
+        ~{"--limits " + limits} \
+        ~{"--kmers " + kmers} \
+        ~{"--dir " + dir} \
+        ~{seqFile}
     }
 
     output {

samtools.wdl

@@ -141,18 +141,18 @@ task view {
     }
 
     command {
-    set -e -o pipefail
-    ~{preCommand}
-    samtools view \
-    ~{"-T " + referenceFasta} \
-    ~{"-o " + outputFileName} \
-    ~{true="-b " false="" outputBam} \
-    ~{true="-u " false="" uncompressedBamOutput} \
-    ~{"-f " + includeFilter} \
-    ~{"-F " + excludeFilter} \
-    ~{"-G " + excludeSpecificFilter} \
-    ~{"--threads " + threads - 1} \
-    ~{inFile}
+        set -e -o pipefail
+        ~{preCommand}
+        samtools view \
+        ~{"-T " + referenceFasta} \
+        ~{"-o " + outputFileName} \
+        ~{true="-b " false="" outputBam} \
+        ~{true="-u " false="" uncompressedBamOutput} \
+        ~{"-f " + includeFilter} \
+        ~{"-F " + excludeFilter} \
+        ~{"-G " + excludeSpecificFilter} \
+        ~{"--threads " + threads - 1} \
+        ~{inFile}
     }
 
     output {

stringtie.wdl

@@ -23,8 +23,7 @@ task Stringtie {
         ~{true="fr" false="" secondStranded} \
         -o ~{assembledTranscriptsFile} \
         ~{"-A " + geneAbundanceFile} \
-        ~{alignedReads} \
-
+        ~{alignedReads}
     }
 
     output {