Merge branch 'spades' of git.lumc.nl:sasc/wdl-tasks into spades

bwa.wdl

@@ -41,6 +41,7 @@ task mem {
     String? I
     command {
         set -e -o pipefail
+        ${"mkdir -p $(dirname " + outputFile + ")"}
         ${preCommand}
         bwa mem \
         ${"-t " + threads } \

centrifuge.wdl

@@ -24,10 +24,7 @@ task download {
     command {
         set -e -o pipefail
         ${preCommand}
-        ${'if [ ! -f ' + seqTaxMapPath +
-        ' ]; then mkdir -p ' + seqTaxMapPath +
-        '; rm -d ' + seqTaxMapPath +
-        '; fi' }
+        ${"mkdir -p $(dirname " + seqTaxMapPath + ")"}
         ${executable} \
         -o ${libraryPath} \
         ${true='-d ' false='' defined(domain)}${sep=','  domain} \
@@ -92,8 +89,7 @@ task build {
     command {
         set -e -o pipefail
         ${preCommand}
-        mkdir -p  ${centrifugeIndexBase}
-        rm -d ${centrifugeIndexBase}
+        ${"mkdir -p $(dirname " + centrifugeIndexBase + ")"}
         ${centrifugeBuildExecutable} \
         ${true='--large-index' false='' largeIndex} \
         ${true='--noauto' false='' noAuto} \

common.wdl

@@ -35,7 +35,7 @@ task concatenateTextFiles {
     Boolean? unzip=false
     command {
         set -e -o pipefail
-        mkdir $(dirname ${combinedFilePath})
+        ${"mkdir -p $(dirname " + combinedFilePath + ")"}
         ${true='zcat' false= 'cat' unzip} ${sep=' ' fileList} \
         > ${combinedFilePath}
     }

cutadapt.wdl

@@ -59,7 +59,9 @@ task cutadapt {
 
     command {
         set -e -o pipefail
-        mkdir -p $(dirname ${read1output})
+        ${"mkdir -p $(dirname " + read1output + ")"}
+        ${"mkdir -p $(dirname " + read2output + ")"}
+        ${"mkdir -p $(dirname " + reportPath + ")"}
         ${preCommand}
         cutadapt \
         ${"--cores=" + cores} \

seqtk.wdl

 task sample {
     File sequenceFile
-    File? outFilePath = "subsampledReads"
+    String? outFilePath = "subsampledReads.fq.gz"
     String? preCommand
     Int? seed
     Boolean? twoPassMode
     Float? fraction
     Int? number
-    Boolean? zip
+    Boolean? zip = true
 
     command {
     set -e -o pipefail
@@ -20,6 +20,6 @@ task sample {
     ${"> " + outFilePath}
     }
     output {
-        File subsampledReads=select_first([outFilePath])
+        File subsampledReads= select_first([outFilePath])
     }
 }
\ No newline at end of file

spades.wdl

@@ -39,8 +39,7 @@ task spades {
         ${true="--rna" false="" rna} \
         ${true="--plasmid" false="" plasmid} \
         ${true="--iontorrent" false="" ionTorrent} \
-        ${"--12 " + interlacedReads }
-        ${"--threads " + threads } \
+        ${"--12 " + interlacedReads } \
         ${"-1 " + read1 } \
         ${"-2 " + read2 } \
         ${"-s " + singleRead } \
@@ -66,12 +65,12 @@ task spades {
         Array[File] correctedReads = glob(outputDir + "/corrected/*.fastq*")
         File scaffolds = outputDir + "/scaffolds.fasta"
         File contigs = outputDir + "/contigs.fasta"
-        File assemblyGraphGfa = outputDir + "/assembly_graph.gfa"
-        File assemblyGraphFastg = outputDir + "/assembly_graph.fastq"
+        File assemblyGraphWithScaffoldsGfa = outputDir + "/assembly_graph_with_scaffolds.gfa"
+        File assemblyGraphFastg = outputDir + "/assembly_graph.fastg"
         File contigsPaths = outputDir + "/contigs.paths"
         File scaffoldsPaths = outputDir + "/scaffolds.paths"
         File params = outputDir + "/params.txt"
-        File log = outputDir + "/spades/log"
+        File log = outputDir + "/spades.log"
     }
     runtime {
         cpu: select_first([threads])