small fixes

bowtie.wdl

@@ -25,7 +25,7 @@ version 1.0
 task Bowtie {
     input {
         Array[File]+ readsUpstream
-        Array[File]+? readsDownstream
+        Array[File] readsDownstream = []
         String outputPath = "mapped.bam"
         Array[File]+ indexFiles
         Int? seedmms
@@ -59,7 +59,7 @@ task Bowtie {
         ~{"--sam-RG '" + samRG}~{true="'" false="" defined(samRG)} \
         ~{sub(indexFiles[0], "(\.rev)?\.[0-9]\.ebwt$", "")} \
         ~{true="-1" false="" defined(readsDownstream)} ~{sep="," readsUpstream} \
-        ~{true="-2" false="" defined(readsDownstream)} ~{sep="," readsDownstream} \
+        ~{true="-2" false="" length(readsDownstream) > 0} ~{sep="," readsDownstream} \
         | picard -Xmx~{picardMemory}G SortSam \
         INPUT=/dev/stdin \
         OUTPUT=~{outputPath} \

cutadapt.wdl

@@ -4,8 +4,8 @@ task Cutadapt {
     input {
         File read1
         File? read2
-        String read1output
-        String? read2output
+        String read1output = "cut_r1.fq.gz"
+        String? read2output = if defined(read2) then "cut_r2.fq.gz" else read2
         String? format
         Array[String]+? adapter
         Array[String]+? front

picard.wdl

@@ -362,34 +362,36 @@ task MergeVCFs {
 task SamToFastq {
     input {
         File inputBam
-        File inputBamIndex
-        String outputRead1
-        String? outputRead2
-        String? outputUnpaired
+        Boolean paired = true
 
         Int memory = 16 # High memory default to avoid crashes.
         Float memoryMultiplier = 3.0
-        String dockerTag = "2.18.26--0"
+        String dockerImage = "quay.io/biocontainers/picard:2.18.26--0"
+        File? NONE
     }
 
+    String outputRead1 = basename(inputBam, "\.[bs]am") + "_R1.fastq.gz"
+    String outputRead2 = basename(inputBam, "\.[bs]am") + "_R2.fastq.gz"
+    String outputUnpaired = basename(inputBam, "\.[bs]am") + "_unpaired.fastq.gz"
+
     command {
         set -e
         picard -Xmx~{memory}G \
         SamToFastq \
         I=~{inputBam} \
         ~{"FASTQ=" + outputRead1} \
-        ~{"SECOND_END_FASTQ=" + outputRead2} \
-        ~{"UNPAIRED_FASTQ=" + outputUnpaired}
+        ~{if paired then "SECOND_END_FASTQ=" + outputRead2 else ""} \
+        ~{if paired then "UNPAIRED_FASTQ=" + outputUnpaired else ""}
     }
 
     output {
         File read1 = outputRead1
-        File? read2 = outputRead2
-        File? unpairedRead = outputUnpaired
+        File? read2 = if paired then outputRead2 else NONE
+        File? unpairedRead = if paired then outputUnpaired else NONE
     }
 
     runtime {
-        docker: "quay.io/biocontainers/picard:" + dockerTag
+        docker: dockerImage
         memory: ceil(memory * memoryMultiplier)
     }
 }

samtools.wdl

@@ -208,8 +208,8 @@ task View {
     input {
         File inFile
         File? referenceFasta
-        String outputFileName
-        Boolean? outputBam
+        String outputFileName = if outputBam then "view.bam" else "view.sam"
+        Boolean outputBam = true
         Boolean? uncompressedBamOutput
         Int? includeFilter
         Int? excludeFilter