add runtime settings

biopet.wdl

@@ -134,4 +134,8 @@ task BaseCounter {
         File transcriptIntronicSense = outputDir + "/" + prefix + ".base.transcript.intronic.sense.counts"
         File transcriptSense = outputDir + "/" + prefix + ".base.transcript.sense.counts"
     }
+
+    runtime {
+        memory: 16
+    }
 }

bwa.wdl

@@ -6,15 +6,23 @@ task BwaMem {
     String outputPath
     String? readgroup
 
+    Int? threads
+    Int? memory
+
     command {
         set -e -o pipefail
         mkdir -p $(dirname ${outputPath})
         ${preCommand}
-        bwa mem ${"-R '" + readgroup + "'"} \
+        bwa mem ${"-t " + threads} \
+        ${"-R '" + readgroup + "'"} \
         ${referenceFasta} ${inputR1} ${inputR2} | samtools sort --output-fmt BAM - > ${outputPath}
     }
 
     output {
         File bamFile = outputPath
     }
+    runtime{
+        threads: select_first([threads])
+        memory: if defined(memory) then memory else 8
+    }
 }

common.wdl

 task objectMd5 {
     Object the_object
+
     command {
         cat ${write_object(the_object)} |  md5sum - | sed -e 's/  -//'
     }
+
     output {
         String md5sum = read_string(stdout())
     }
+
+    runtime {
+        memory: 1
+    }
 }
 
 task mapMd5 {
     Map[String,String] map
+
     command {
-    cat ${write_map(map)} | md5sum - | sed -e 's/  -//'
+        cat ${write_map(map)} | md5sum - | sed -e 's/  -//'
     }
+
     output {
         String md5sum = read_string(stdout())
     }
+
+    runtime {
+        memory: 1
+    }
 }
 
 task stringArrayMd5 {
     Array[String] stringArray
+
     command {
-    set -eu -o pipefail
-    echo ${sep=',' stringArray} | md5sum - | sed -e 's/  -//'
+        set -eu -o pipefail
+        echo ${sep=',' stringArray} | md5sum - | sed -e 's/  -//'
     }
+
     output {
-    String md5sum = read_string(stdout())
+        String md5sum = read_string(stdout())
+    }
+
+    runtime {
+        memory: 1
     }
 }
 
@@ -33,37 +51,55 @@ task concatenateTextFiles {
     Array[File] fileList
     String combinedFilePath
     Boolean? unzip=false
+
     command {
         mkdir -p ${combinedFilePath}
         rm -d ${combinedFilePath}
         ${true='zcat' false= 'cat' unzip} ${sep=' ' fileList} \
         > ${combinedFilePath}
     }
+
     output {
         File combinedFile = combinedFilePath
     }
+
+    runtime {
+        memory: 1
+    }
 }
 
 # inspired by https://gatkforums.broadinstitute.org/wdl/discussion/9616/is-there-a-way-to-flatten-arrays
 task flattenStringArray {
     Array[Array[String]] arrayList
+
     command {
-    for line in $(echo ${sep=', ' arrayList}) ; \
-    do echo $line | tr -d '"[],' ; done
+        for line in $(echo ${sep=', ' arrayList}) ; \
+        do echo $line | tr -d '"[],' ; done
     }
+
     output {
         Array[String] flattenedArray = read_lines(stdout())
     }
+
+    runtime {
+        memory: 1
+    }
 }
 
 task appendToStringArray {
     Array[String] array
     String string
+
     command {
         echo "${sep='\n' array}
         ${string}"
     }
+
     output {
         Array[String] out_array = read_lines(stdout())
     }
+
+    runtime {
+        memory: 1
+    }
 }
\ No newline at end of file

fastqc.wdl

@@ -87,15 +87,21 @@ task extractAdapters {
 task getConfiguration {
     String? preCommand
     String? fastqcDirFile = "fastqcDir.txt"
+
     command {
         set -e -o pipefail
         ${preCommand}
         echo $(dirname $(readlink -f $(which fastqc))) > ${fastqcDirFile}
     }
+
     output {
         String fastqcDir = read_string(fastqcDirFile)
         File adapterList = fastqcDir + "/Configuration/adapter_list.txt"
         File contaminantList = fastqcDir + "/Configuration/contaminant_list.txt"
         File limits = fastqcDir + "/Configuration/limits.txt"
     }
+
+    runtime {
+        memory: 1
+    }
 }
\ No newline at end of file

gatk.wdl

@@ -24,9 +24,14 @@ task BaseRecalibrator {
           --known-sites ${sep=" --known-sites " known_indels_sites_VCFs} \
           -L ${sep=" -L " sequence_group_interval}
     }
+
     output {
         File recalibration_report = "${recalibration_report_filename}"
     }
+
+    runtime {
+        memory: 6
+    }
 }
 
 # Apply Base Quality Score Recalibration (BQSR) model
@@ -57,10 +62,15 @@ task ApplyBQSR {
           --static-quantized-quals 10 --static-quantized-quals 20 --static-quantized-quals 30 \
           -L ${sep=" -L " sequence_group_interval}
     }
+
     output {
         File recalibrated_bam = "${output_bam_path}"
         File recalibrated_bam_checksum = "${output_bam_path}.md5"
     }
+
+    runtime {
+        memory: 6
+    }
 }
 
 # Combine multiple recalibration tables from scattered BaseRecalibrator runs
@@ -78,9 +88,14 @@ task GatherBqsrReports {
         -I ${sep=' -I ' input_bqsr_reports} \
         -O ${output_report_filepath}
     }
+
     output {
         File output_bqsr_report = "${output_report_filepath}"
     }
+
+    runtime {
+        memory: 4
+    }
 }
 
 # Call variants on a single sample with HaplotypeCaller to produce a GVCF
@@ -109,10 +124,15 @@ task HaplotypeCallerGvcf {
           -contamination ${default=0 contamination} \
           -ERC GVCF
     }
+
     output {
         File output_gvcf = "${gvcf_basename}.vcf.gz"
         File output_gvcf_index = "${gvcf_basename}.vcf.gz.tbi"
     }
+
+    runtime {
+        memory: 6
+    }
 }
 
 task GenotypeGVCFs {
@@ -154,6 +174,10 @@ task GenotypeGVCFs {
         File output_vcf = output_basename + ".vcf.gz"
         File output_vcf_index = output_basename + ".vcf.gz.tbi"
     }
+
+    runtime{
+        memory: 6
+    }
 }
 
 task CombineGVCFs {
@@ -193,6 +217,10 @@ task CombineGVCFs {
         File output_gvcf = output_basename + ".vcf.gz"
         File output_gvcf_index = output_basename + ".vcf.gz.tbi"
     }
+
+    runtime {
+        memory: 6
+    }
 }
 
 task SplitNCigarReads {
@@ -221,4 +249,8 @@ task SplitNCigarReads {
         File bam = output_bam
         File bam_index = output_bam + ".bai"
     }
+
+    runtime {
+        memory: 6
+    }
 }

htseq.wdl

@@ -22,4 +22,8 @@ task HTSeqCount {
     output {
         File counts = outputTable
     }
+
+    runtime {
+        memory: 3
+    }
 }
\ No newline at end of file

mergecounts.wdl

@@ -32,4 +32,8 @@ task MergeCounts {
     output {
         File mergedCounts = outputFile
     }
+
+    runtime {
+        memory: 4 + (2*length(inputFiles))
+    }
 }
\ No newline at end of file

picard.wdl

@@ -17,10 +17,15 @@ task ScatterIntervalList {
           INPUT=${interval_list} \
           OUTPUT=scatter_list
     }
+
     output {
         Array[File] out = glob("scatter_list/*/*.interval_list")
         Int interval_count = read_int(stdout())
     }
+
+    runtime {
+        memory: 6
+    }
 }
 
 # Combine multiple recalibrated BAM files from scattered ApplyRecalibration runs
@@ -41,11 +46,16 @@ task GatherBamFiles {
           CREATE_INDEX=true \
           CREATE_MD5_FILE=true
     }
+
     output {
         File output_bam = "${output_bam_path}"
         File output_bam_index = sub(output_bam_path, ".bam$", ".bai")
         File output_bam_md5 = "${output_bam_path}.md5"
     }
+
+    runtime {
+        memory: 6
+    }
 }
 
 # Mark duplicate reads to avoid counting non-independent observations
@@ -81,11 +91,16 @@ task MarkDuplicates {
           CREATE_INDEX=true \
           ADD_PG_TAG_TO_READS=false
     }
+
     output {
         File output_bam = output_bam_path
         File output_bam_index = sub(output_bam_path, ".bam$", ".bai")
         File duplicate_metrics = metrics_path
     }
+
+    runtime {
+        memory: 6
+    }
 }
 
 # Combine multiple VCFs or GVCFs from scattered HaplotypeCaller runs
@@ -107,8 +122,13 @@ task MergeVCFs {
           INPUT=${sep=' INPUT=' input_vcfs} \
           OUTPUT=${output_vcf_path}
     }
+
     output {
         File output_vcf = output_vcf_path
         File output_vcf_index = output_vcf_path + ".tbi"
     }
+
+    runtime {
+        memory: 6
+    }
 }
\ No newline at end of file

star.wdl

@@ -37,6 +37,7 @@ task Star {
     }
 
     runtime {
-        threads: runThreadN
+        threads: select_first([runThreadN])
+        memory: 10
     }
 }
\ No newline at end of file

stringtie.wdl

@@ -28,6 +28,6 @@ task Stringtie {
     }
 
     runtime {
-        threads: threads
+        threads: select_first([threads])
     }
 }
\ No newline at end of file