Merge branch 'master' into centrifuge-classify

biopet.wdl

@@ -84,10 +84,9 @@ task SampleConfig {
     }
 
     output {
-        Array[String] keys = read_lines(stdout())
+        File keysFile = stdout()
         File? jsonOutput = jsonOutputPath
         File? tsvOutput = tsvOutputPath
-        Object values = if (defined(tsvOutput) && size(tsvOutput) > 0) then read_map(tsvOutput) else { "": "" }
     }
 
     runtime {

flash.wdl

+task flash {
+    String? preCommand
+    File inputR1
+    File inputR2
+    String outdirPath
+    String? outPrefix = "flash"
+    Int? minOverlap
+    Int? maxOverlap
+    Boolean? compress = true
+    Int? threads
+    Int? memory
+
+    command {
+        set -e -o pipefail
+        mkdir -p ${outdirPath}
+        ${preCommand}
+        flash \
+        ${"--threads=" + threads} \
+        ${"--output-directory=" + outdirPath} \
+        ${"--output-prefix=" + outPrefix} \
+        ${true="--compress " false="" defined(compress)} \
+        ${"--min-overlap=" + minOverlap} \
+        ${"--max-overlap=" + maxOverlap} \
+        ${inputR1} ${inputR2}
+    }
+
+    output {
+        File extendedFrags = outdirPath + "/" + outPrefix + ".extendedFrags.fastq.gz"
+        File notCombined1 = outdirPath + "/" + outPrefix + ".notCombined_1.fastq.gz"
+        File notCombined2 = outdirPath + "/" + outPrefix + ".notCombined_2.fastq.gz"
+        File hist = outdirPath + "/" + outPrefix + ".hist"
+        File histogram = outdirPath + "/" + outPrefix + ".histogram"
+    }
+
+    runtime {
+        cpu: select_first([threads, 2])
+        memory: select_first([memory, 2])
+    }
+
+}
\ No newline at end of file

gatk.wdl

@@ -253,6 +253,7 @@ task SplitNCigarReads {
     String? preCommand
 
     File input_bam
+    File input_bam_index
     File ref_fasta
     File ref_fasta_index
     File ref_dict
@@ -271,13 +272,13 @@ task SplitNCigarReads {
         SplitNCigarReads \
         -I ${input_bam} \
         -R ${ref_fasta} \
-        -O ${output_bam} # might have to be -o depending on GATK version \
+        -O ${output_bam} \
         -L ${sep=' -L ' intervals}
     }
 
     output {
         File bam = output_bam
-        File bam_index = output_bam + ".bai"
+        File bam_index = sub(output_bam, "\\.bam$", ".bai")
     }
 
     runtime {

star.wdl

@@ -12,6 +12,7 @@ task Star {
     String? outStd
     String? twopassMode
     Array[String]? outSAMattrRGline
+    Int? limitBAMsortRAM
 
     Int? memory
 
@@ -34,6 +35,7 @@ task Star {
         ${"--runThreadN " + runThreadN} \
         ${"--outStd " + outStd} \
         ${"--twopassMode " + twopassMode} \
+        ${"--limitBAMsortRAM " + limitBAMsortRAM} \
         ${true="--outSAMattrRGline " false="" defined(outSAMattrRGline)} ${sep=" , " outSAMattrRGline}
     }