a few more linting things

common.wdl

@@ -121,7 +121,8 @@ task MapMd5 {
     }
 
     command {
-        cat ~{write_map(map)} | md5sum - | sed -e 's/  -//'
+        set -e -o pipefail
+        md5sum "~{write_map(map)}" | cut -f 1 -d ' '
     }
 
     output {

fastqc.wdl

@@ -145,7 +145,9 @@ task GetConfiguration {
 
     command <<<
         set -e
-        fastqcDir=$(dirname $(readlink -f $(which fastqc)))
+        fastqcExe="$(command -v fastqc)"
+        fastqcPath="$(readlink -f $fastqcExe)"
+        fastqcDir="$(dirname $fastqcPath)"
         mkdir Configuration
         cp ${fastqcDir}/Configuration/adapter_list.txt Configuration/adapter_list.txt
         cp ${fastqcDir}/Configuration/contaminant_list.txt Configuration/contaminant_list.txt

gatk.wdl

@@ -530,16 +530,15 @@ task CombineVariants {
 
         # build "-V:<ID> <file.vcf>" arguments according to IDs and VCFs to merge
         # Make sure commands are run in bash
-        bash -c '#!/usr/bin/env bash
-        set -eux
+        V_args=$(bash -c '
+        set -eu
         ids=(~{sep=" " identifiers})
         vars=(~{sep=" " variantVcfs})
-        V_args=$(
-            for (( i = 0; i < ${#ids[@]}; ++i ))
-              do
-                printf -- "-V:%s %s " "${ids[i]}" "${vars[i]}"
-              done
-        )
+        for (( i = 0; i < ${#ids[@]}; ++i ))
+          do
+            printf -- "-V:%s %s " "${ids[i]}" "${vars[i]}"
+          done
+        ')
         java -Xmx~{javaXmx} -jar ~{installDir}/GenomeAnalysisTK.jar \
         -T CombineVariants \
         -R ~{referenceFasta} \
@@ -547,7 +546,6 @@ task CombineVariants {
         --filteredrecordsmergetype ~{filteredRecordsMergeType} \
         --out ~{outputPath} \
         $V_args
-        '
     >>>
 
     output {

gffcompare.wdl

@@ -31,8 +31,8 @@ task GffCompare {
         File? noneFile # This is a wdl workaround. Please do not assign!
     }
     # This allows for the creation of output directories
-    String dirPrefix= if defined(outputDir)
-        then outputDir + "/"
+    String dirPrefix = if defined(outputDir)
+        then select_first([outputDir]) + "/"
         else ""
     String totalPrefix = dirPrefix + outPrefix