alphabetic ordering

biopet.wdl

+# PLEASE ADD TASKS IN ALPHABETIC ORDER.
+# This makes searching a lot easier.
+task BaseCounter {
+    String? preCommand
+    String tool_jar #Should this be of type File?
+    File bam
+    File refFlat
+    String outputDir
+    String prefix
+
+    Float? memory
+    Float? memoryMultiplier
+
+    Int mem = ceil(select_first([memory, 12.0]))
+    command {
+        set -e -o pipefail
+        ${preCommand}
+        mkdir -p ${outputDir}
+        java -Xmx${mem}G -jar ${tool_jar} \
+        -b ${bam} \
+        -r ${refFlat} \
+        -o ${outputDir} \
+        -p ${prefix}
+    }
+
+    output {
+        File exonAntisense = outputDir + "/" + prefix + ".base.exon.antisense.counts"
+        File exon = outputDir + "/" + prefix + ".base.exon.counts"
+        File exonMergeAntisense = outputDir + "/" + prefix + ".base.exon.merge.antisense.counts"
+        File exonMerge = outputDir + "/" + prefix + ".base.exon.merge.counts"
+        File exonMergeSense = outputDir + "/" + prefix + ".base.exon.merge.sense.counts"
+        File exonSense = outputDir + "/" + prefix + ".base.exon.sense.counts"
+        File geneAntisense = outputDir + "/" + prefix + ".base.gene.antisense.counts"
+        File gene = outputDir + "/" + prefix + ".base.gene.counts"
+        File geneExonicAntisense = outputDir + "/" + prefix + ".base.gene.exonic.antisense.counts"
+        File geneExonic = outputDir + "/" + prefix + ".base.gene.exonic.counts"
+        File geneExonicSense = outputDir + "/" + prefix + ".base.gene.exonic.sense.counts"
+        File geneIntronicAntisense = outputDir + "/" + prefix + ".base.gene.intronic.antisense.counts"
+        File geneIntronic = outputDir + "/" + prefix + ".base.gene.intronic.counts"
+        File geneIntronicSense = outputDir + "/" + prefix + ".base.gene.intronic.sense.counts"
+        File geneSense = outputDir + "/" + prefix + ".base.gene.sense.counts"
+        File intronAntisense = outputDir + "/" + prefix + ".base.intron.antisense.counts"
+        File intron = outputDir + "/" + prefix + ".base.intron.counts"
+        File intronMergeAntisense = outputDir + "/" + prefix + ".base.intron.merge.antisense.counts"
+        File intronMerge = outputDir + "/" + prefix + ".base.intron.merge.counts"
+        File intronMergeSense = outputDir + "/" + prefix + ".base.intron.merge.sense.counts"
+        File intronSense = outputDir + "/" + prefix + ".base.intron.sense.counts"
+        File metaExonsNonStranded = outputDir + "/" + prefix + ".base.metaexons.non_stranded.counts"
+        File metaExonsStrandedAntisense = outputDir + "/" + prefix + ".base.metaexons.stranded.antisense.counts"
+        File metaExonsStranded = outputDir + "/" + prefix + ".base.metaexons.stranded.counts"
+        File metaExonsStrandedSense = outputDir + "/" + prefix + ".base.metaexons.stranded.sense.counts"
+        File transcriptAntisense = outputDir + "/" + prefix + ".base.transcript.antisense.counts"
+        File transcript = outputDir + "/" + prefix + ".base.transcript.counts"
+        File transcriptExonicAntisense = outputDir + "/" + prefix + ".base.transcript.exonic.antisense.counts"
+        File transcriptExonic = outputDir + "/" + prefix + ".base.transcript.exonic.counts"
+        File transcriptExonicSense = outputDir + "/" + prefix + ".base.transcript.exonic.sense.counts"
+        File transcriptIntronicAntisense = outputDir + "/" + prefix + ".base.transcript.intronic.antisense.counts"
+        File transcriptIntronic = outputDir + "/" + prefix + ".base.transcript.intronic.counts"
+        File transcriptIntronicSense = outputDir + "/" + prefix + ".base.transcript.intronic.sense.counts"
+        File transcriptSense = outputDir + "/" + prefix + ".base.transcript.sense.counts"
+    }
+
+    runtime {
+        memory: ceil(mem * select_first([memoryMultiplier, 1.5]))
+    }
+}
+
 task FastqSplitter {
     String? preCommand
     File inputFastq
@@ -23,39 +90,6 @@ task FastqSplitter {
     }
 }
 
-task ScatterRegions {
-    String? preCommand
-    File ref_fasta
-    File ref_dict
-    String outputDirPath
-    String tool_jar
-    Int? scatterSize
-    File? regions
-
-    Float? memory
-    Float? memoryMultiplier
-
-    Int mem = ceil(select_first([memory, 4.0]))
-    command {
-        set -e -o pipefail
-        ${preCommand}
-        mkdir -p ${outputDirPath}
-        java -Xmx${mem}G -jar ${tool_jar} \
-          -R ${ref_fasta} \
-          -o ${outputDirPath} \
-          ${"-s " + scatterSize} \
-          ${"-L " + regions}
-    }
-
-    output {
-        Array[File] scatters = glob(outputDirPath + "/scatter-*.bed")
-    }
-
-    runtime {
-        memory: ceil(mem * select_first([memoryMultiplier, 2.0]))
-    }
-}
-
 task SampleConfig {
     String? preCommand
     String tool_jar
@@ -95,67 +129,36 @@ task SampleConfig {
     }
 }
 
-task BaseCounter {
+task ScatterRegions {
     String? preCommand
-    String tool_jar #Should this be of type File?
-    File bam
-    File refFlat
-    String outputDir
-    String prefix
+    File ref_fasta
+    File ref_dict
+    String outputDirPath
+    String tool_jar
+    Int? scatterSize
+    File? regions
 
     Float? memory
     Float? memoryMultiplier
 
-    Int mem = ceil(select_first([memory, 12.0]))
+    Int mem = ceil(select_first([memory, 4.0]))
     command {
         set -e -o pipefail
         ${preCommand}
-        mkdir -p ${outputDir}
+        mkdir -p ${outputDirPath}
         java -Xmx${mem}G -jar ${tool_jar} \
-        -b ${bam} \
-        -r ${refFlat} \
-        -o ${outputDir} \
-        -p ${prefix}
+          -R ${ref_fasta} \
+          -o ${outputDirPath} \
+          ${"-s " + scatterSize} \
+          ${"-L " + regions}
     }
 
     output {
-        File exonAntisense = outputDir + "/" + prefix + ".base.exon.antisense.counts"
-        File exon = outputDir + "/" + prefix + ".base.exon.counts"
-        File exonMergeAntisense = outputDir + "/" + prefix + ".base.exon.merge.antisense.counts"
-        File exonMerge = outputDir + "/" + prefix + ".base.exon.merge.counts"
-        File exonMergeSense = outputDir + "/" + prefix + ".base.exon.merge.sense.counts"
-        File exonSense = outputDir + "/" + prefix + ".base.exon.sense.counts"
-        File geneAntisense = outputDir + "/" + prefix + ".base.gene.antisense.counts"
-        File gene = outputDir + "/" + prefix + ".base.gene.counts"
-        File geneExonicAntisense = outputDir + "/" + prefix + ".base.gene.exonic.antisense.counts"
-        File geneExonic = outputDir + "/" + prefix + ".base.gene.exonic.counts"
-        File geneExonicSense = outputDir + "/" + prefix + ".base.gene.exonic.sense.counts"
-        File geneIntronicAntisense = outputDir + "/" + prefix + ".base.gene.intronic.antisense.counts"
-        File geneIntronic = outputDir + "/" + prefix + ".base.gene.intronic.counts"
-        File geneIntronicSense = outputDir + "/" + prefix + ".base.gene.intronic.sense.counts"
-        File geneSense = outputDir + "/" + prefix + ".base.gene.sense.counts"
-        File intronAntisense = outputDir + "/" + prefix + ".base.intron.antisense.counts"
-        File intron = outputDir + "/" + prefix + ".base.intron.counts"
-        File intronMergeAntisense = outputDir + "/" + prefix + ".base.intron.merge.antisense.counts"
-        File intronMerge = outputDir + "/" + prefix + ".base.intron.merge.counts"
-        File intronMergeSense = outputDir + "/" + prefix + ".base.intron.merge.sense.counts"
-        File intronSense = outputDir + "/" + prefix + ".base.intron.sense.counts"
-        File metaExonsNonStranded = outputDir + "/" + prefix + ".base.metaexons.non_stranded.counts"
-        File metaExonsStrandedAntisense = outputDir + "/" + prefix + ".base.metaexons.stranded.antisense.counts"
-        File metaExonsStranded = outputDir + "/" + prefix + ".base.metaexons.stranded.counts"
-        File metaExonsStrandedSense = outputDir + "/" + prefix + ".base.metaexons.stranded.sense.counts"
-        File transcriptAntisense = outputDir + "/" + prefix + ".base.transcript.antisense.counts"
-        File transcript = outputDir + "/" + prefix + ".base.transcript.counts"
-        File transcriptExonicAntisense = outputDir + "/" + prefix + ".base.transcript.exonic.antisense.counts"
-        File transcriptExonic = outputDir + "/" + prefix + ".base.transcript.exonic.counts"
-        File transcriptExonicSense = outputDir + "/" + prefix + ".base.transcript.exonic.sense.counts"
-        File transcriptIntronicAntisense = outputDir + "/" + prefix + ".base.transcript.intronic.antisense.counts"
-        File transcriptIntronic = outputDir + "/" + prefix + ".base.transcript.intronic.counts"
-        File transcriptIntronicSense = outputDir + "/" + prefix + ".base.transcript.intronic.sense.counts"
-        File transcriptSense = outputDir + "/" + prefix + ".base.transcript.sense.counts"
+        Array[File] scatters = glob(outputDirPath + "/scatter-*.bed")
     }
 
     runtime {
-        memory: ceil(mem * select_first([memoryMultiplier, 1.5]))
+        memory: ceil(mem * select_first([memoryMultiplier, 2.0]))
     }
 }
+