spades to 1.0

spades.wdl

+version 1.0
+
 task spades {
-    String outputDir
-    String? preCommand
-    File read1
-    File? read2
-    File? interlacedReads
-    File? sangerReads
-    File? pacbioReads
-    File? nanoporeReads
-    File? tslrContigs
-    File? trustedContigs
-    File? untrustedContigs
-    Boolean? singleCell
-    Boolean? metagenomic
-    Boolean? rna
-    Boolean? plasmid
-    Boolean? ionTorrent
-    Boolean? onlyErrorCorrection
-    Boolean? onlyAssembler
-    Boolean? careful
-    Boolean? disableGzipOutput
-    Boolean? disableRepeatResolution
-    File? dataset
-    Int? threads
-    Float? memoryGb
-    File? tmpDir
-    String? k
-    Float? covCutoff
-    Int? phredOffset
+    input {
+        String outputDir
+        String? preCommand
+        File read1
+        File? read2
+        File? interlacedReads
+        File? sangerReads
+        File? pacbioReads
+        File? nanoporeReads
+        File? tslrContigs
+        File? trustedContigs
+        File? untrustedContigs
+        Boolean? singleCell
+        Boolean? metagenomic
+        Boolean? rna
+        Boolean? plasmid
+        Boolean? ionTorrent
+        Boolean? onlyErrorCorrection
+        Boolean? onlyAssembler
+        Boolean? careful
+        Boolean? disableGzipOutput
+        Boolean? disableRepeatResolution
+        File? dataset
+        Int? threads
+        Float? memoryGb
+        File? tmpDir
+        String? k
+        Float? covCutoff
+        Int? phredOffset
+    }
     Int finalThreads = select_first([threads,1])
     Float totalMemory = select_first([memoryGb, finalThreads * 16.0])
     Int finalMemory = ceil(totalMemory)
@@ -34,34 +38,34 @@ task spades {
 
     command {
         set -e -o pipefail
-        ${preCommand}
+        ~{preCommand}
         spades.py \
-        ${"-o " + outputDir} \
-        ${true="--sc" false="" singleCell} \
-        ${true="--meta" false="" metagenomic} \
-        ${true="--rna" false="" rna} \
-        ${true="--plasmid" false="" plasmid} \
-        ${true="--iontorrent" false="" ionTorrent} \
-        ${"--12 " + interlacedReads } \
-        ${true="-1" false="-s" defined(read2)} ${read1}  \
-        ${"-2 " + read2 } \
-        ${"--sanger " + sangerReads } \
-        ${"--pacbio " + pacbioReads } \
-        ${"--nanopore " + nanoporeReads } \
-        ${"--tslr " + tslrContigs } \
-        ${"--trusted-contigs " + trustedContigs } \
-        ${"--untrusted-contigs " + untrustedContigs } \
-        ${true="--only-error-correction" false="" onlyErrorCorrection } \
-        ${true="--only-assembler" false="" onlyAssembler } \
-        ${true="--careful" false="" careful } \
-        ${true="--disable-gzip-output" false="" disableGzipOutput} \
-        ${true="--disable-rr" false="" disableRepeatResolution } \
-        ${"--dataset " + dataset } \
-        ${"--threads " + finalThreads} \
-        ${"--memory " + finalMemory } \
-        ${"-k " + k } \
-        ${"--cov-cutoff " + covCutoff } \
-        ${"--phred-offset " + phredOffset }
+        ~{"-o " + outputDir} \
+        ~{true="--sc" false="" singleCell} \
+        ~{true="--meta" false="" metagenomic} \
+        ~{true="--rna" false="" rna} \
+        ~{true="--plasmid" false="" plasmid} \
+        ~{true="--iontorrent" false="" ionTorrent} \
+        ~{"--12 " + interlacedReads } \
+        ~{true="-1" false="-s" defined(read2)} ~{read1}  \
+        ~{"-2 " + read2 } \
+        ~{"--sanger " + sangerReads } \
+        ~{"--pacbio " + pacbioReads } \
+        ~{"--nanopore " + nanoporeReads } \
+        ~{"--tslr " + tslrContigs } \
+        ~{"--trusted-contigs " + trustedContigs } \
+        ~{"--untrusted-contigs " + untrustedContigs } \
+        ~{true="--only-error-correction" false="" onlyErrorCorrection } \
+        ~{true="--only-assembler" false="" onlyAssembler } \
+        ~{true="--careful" false="" careful } \
+        ~{true="--disable-gzip-output" false="" disableGzipOutput} \
+        ~{true="--disable-rr" false="" disableRepeatResolution } \
+        ~{"--dataset " + dataset } \
+        ~{"--threads " + finalThreads} \
+        ~{"--memory " + finalMemory } \
+        ~{"-k " + k } \
+        ~{"--cov-cutoff " + covCutoff } \
+        ~{"--phred-offset " + phredOffset }
     }
     output {
         Array[File] correctedReads = glob(outputDir + "/corrected/*.fastq*")