Merge pull request #85 from biowdl/PYT-8

Make tasks suitable for running against relative paths.

CPAT.wdl

@@ -5,8 +5,8 @@ task CPAT {
         String? preCommand
         File gene
         String outFilePath
-        String hex
-        String logitModel
+        File hex
+        File logitModel
         File? referenceGenome
         File? referenceGenomeIndex  # Should be added as input if
         # CPAT should not index the reference genome.

biopet/bamstats.wdl

@@ -19,12 +19,12 @@ task Generate {
         Float memoryMultiplier = 2.0
     }
 
+    File referenceFasta = if defined(reference) then select_first([reference]).fasta else ""
+
     String toolCommand = if defined(toolJar)
         then "java -Xmx" + memory + "G -jar " + toolJar
         else "biopet-bamstats -Xmx" + memory + "G"
 
-    String refArg = if (defined(reference)) then "--reference " + select_first([reference]).fasta else ""
-
     command {
         set -e -o pipefail
         ~{preCommand}
@@ -32,7 +32,7 @@ task Generate {
         ~{toolCommand} Generate \
         --bam ~{bam.file} \
         ~{"--bedFile " + bedFile} \
-        ~{refArg} \
+        ~{true="--reference" false="" defined(reference)} ~{referenceFasta} \
         ~{true="--onlyUnmapped" false="" onlyUnmapped} \
         ~{true="--scatterMode" false="" scatterMode} \
         ~{true="--tsvOutputs" false="" tsvOutputs} \

biopet/biopet.wdl

@@ -325,7 +325,6 @@ task ValidateFastq {
 
     output {
         File stderr = stderr()
-        FastqPair validatedFastq = inputFastq
     }
 
     runtime {

common.wdl

@@ -146,6 +146,8 @@ task YamlToJson {
     }
 
     command {
+        set -e
+        mkdir -p $(dirname ~{outputJson})
         python <<CODE
         import json
         import yaml

gatk.wdl

@@ -196,7 +196,7 @@ task GenotypeGVCFs {
         Float memoryMultiplier = 2.0
     }
 
-    String dbsnpArg = if defined(dbsnpVCF) then "-D " + select_first([dbsnpVCF]).file else ""
+    File dbsnpFile = if (defined(dbsnpVCF)) then select_first([dbsnpVCF]).file else ""
 
     String toolCommand = if defined(gatkJar)
         then "java -Xmx" + memory + "G -jar " + gatkJar
@@ -209,7 +209,7 @@ task GenotypeGVCFs {
         GenotypeGVCFs \
         -R ~{reference.fasta} \
         -O ~{outputPath} \
-        ~{dbsnpArg} \
+        ~{true="-D" false="" defined(dbsnpVCF)} ~{dbsnpFile} \
         -G StandardAnnotation \
         --only-output-calls-starting-in-intervals \
         -new-qual \
@@ -247,7 +247,7 @@ task HaplotypeCallerGvcf {
         Float memoryMultiplier = 3
     }
 
-    String dbsnpArg = if (defined(dbsnpVCF)) then "-D " + select_first([dbsnpVCF]).file else ""
+    File dbsnpFile = if (defined(dbsnpVCF)) then select_first([dbsnpVCF]).file else ""
 
     String toolCommand = if defined(gatkJar)
         then "java -Xmx" + memory + "G -jar " + gatkJar
@@ -262,7 +262,7 @@ task HaplotypeCallerGvcf {
         -O ~{gvcfPath} \
         -I ~{sep=" -I " inputBams} \
         -L ~{sep=' -L ' intervalList} \
-        ~{dbsnpArg} \
+        ~{true="-D" false="" defined(dbsnpVCF)} ~{dbsnpFile} \
         -contamination ~{contamination} \
         -ERC GVCF
     }

star.wdl

@@ -6,7 +6,7 @@ task Star {
 
         Array[File] inputR1
         Array[File]? inputR2
-        String genomeDir
+        File genomeDir
         String outFileNamePrefix
 
         String outSAMtype = "BAM SortedByCoordinate"