add preCommand

centrifuge.wdl

@@ -6,7 +6,7 @@ task download {
     String libraryPath
     Array[String]? domain
     String? executable = "centrifuge-download"
-    File? condaEnvironment
+    String? preCommand
     String? seqTaxMapPath
     String? database = "refseq"
     String? assemblyLevel
@@ -22,11 +22,12 @@ task download {
     # The bash statement at the beginning is to make sure
     # the directory for the SeqTaxMapPath exists.
     command {
+        set -e -o pipefail
+        ${preCommand}
         ${'if [ ! -f ' + seqTaxMapPath +
         ' ]; then mkdir -p ' + seqTaxMapPath +
         '; rm -d ' + seqTaxMapPath +
         '; fi' }
-        ${"source activate " + condaEnvironment}
         ${executable} \
         -o ${libraryPath} \
         ${true='-d ' false='' defined(domain)}${sep=','  domain} \
@@ -50,9 +51,10 @@ task download {
 task downloadTaxonomy {
     String centrifugeTaxonomyDir
     String? executable = "centrifuge-download"
-    File? condaEnvironment
+    String? preCommand
     command {
-        ${"source activate " + condaEnvironment}
+        set -e -o pipefail
+        ${preCommand}
         ${executable} \
         -o ${centrifugeTaxonomyDir} \
         taxonomy
@@ -69,7 +71,7 @@ task build {
     File taxonomyTree
     File inputFasta
     String centrifugeIndexBase
-    File? condaEnvironment
+    String? preCommand
     String? centrifugeBuildExecutable = "centrifuge-build"
     #Boolean? c = false
     Boolean? largeIndex = false
@@ -88,9 +90,10 @@ task build {
     Int? kmerCount
 
     command {
+        set -e -o pipefail
+        ${preCommand}
         mkdir -p  ${centrifugeIndexBase}
         rm -d ${centrifugeIndexBase}
-        ${"source activate " + condaEnvironment}
         ${centrifugeBuildExecutable} \
         ${true='--large-index' false='' largeIndex} \
         ${true='--noauto' false='' noAuto} \

cutadapt.wdl

@@ -4,7 +4,7 @@ task cutadapt {
     String read1output
     String? read2output
     String? format
-    String? condaEnv
+    String? preCommand
     Int? cores = 1
     Array[String]? adapter
     Array[String]? front
@@ -57,7 +57,7 @@ task cutadapt {
 
     command {
         set -e -o pipefail
-        ${"source activate " + condaEnv}
+        ${preCommand}
         cutadapt \
         ${"--cores=" + cores} \
         ${true="-a " false="" defined(adapter)} ${sep=" -a " adapter} \

fastqc.wdl

 task fastqc {
     File seqFile
     String outdirPath
-    String? condaEnv
+    String? preCommand
     Boolean? casava
     Boolean? nano
     Boolean? noFilter
@@ -18,7 +18,7 @@ task fastqc {
 
     command {
     set -e -o pipefail
-    ${"source activate " + condaEnv}
+    ${preCommand}
     mkdir -p ${outdirPath}
     fastqc \
     ${"--outdir " + outdirPath} \

ncbi.wdl

@@ -14,11 +14,11 @@ task genomeDownload {
     String? domain = "all"
 
     String? executable = "ncbi-genome-download"
-    File? condaEnvironment
+    String? preCommand
 
     command {
         set -e -o pipefail
-        ${"source activate " + condaEnvironment}
+        ${preCommand}
         ${executable} \
         ${"--section " + section} \
         ${"--format " + format} \