fastqc to 1.0

fastqc.wdl

+version 1.0
+
 task fastqc {
-    File seqFile
-    String outdirPath
-    String? preCommand
-    Boolean? casava
-    Boolean? nano
-    Boolean? noFilter
-    Boolean? extract = true
-    Boolean? nogroup
-    Int? minLength
-    String? format
-    Int? threads = 1
-    File? contaminants
-    File? adapters
-    File? limits
-    Int? kmers
-    String? dir
+    input {
+        File seqFile
+        String outdirPath
+        String? preCommand
+        Boolean? casava
+        Boolean? nano
+        Boolean? noFilter
+        Boolean? extract = true
+        Boolean? nogroup
+        Int? minLength
+        String? format
+        Int? threads = 1
+        File? contaminants
+        File? adapters
+        File? limits
+        Int? kmers
+        String? dir
+    }
     # Chops of the .gz extension if present.
     String name = sub(seqFile, "\\.gz$","")
     # This regex chops of the extension and replaces it with _fastqc for the reportdir.
@@ -22,24 +26,24 @@ task fastqc {
     String reportDir = outdirPath + "/" + sub(basename(name), "\\.[^\\.]*$", "_fastqc")
     command {
     set -e -o pipefail
-    ${preCommand}
-    mkdir -p ${outdirPath}
+    ~{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}
+    ~{"--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}
 
     }
 
@@ -56,13 +60,14 @@ task fastqc {
 }
 
 task getConfiguration {
-    String? preCommand
-    String? fastqcDirFile = "fastqcDir.txt"
-
+    input {
+        String? preCommand
+        String? fastqcDirFile = "fastqcDir.txt"
+    }
     command {
         set -e -o pipefail
-        ${preCommand}
-        echo $(dirname $(readlink -f $(which fastqc))) > ${fastqcDirFile}
+        ~{preCommand}
+        echo $(dirname $(readlink -f $(which fastqc))) > ~{fastqcDirFile}
     }
 
     output {