Merge pull request #71 from biowdl/BIOWDL-126

Add gffcompare

gffcompare.wdl

+version 1.0
+
+task GffCompare {
+    input {
+        String? preCommand
+        File? inputGtfList
+        Array[File] inputGtfFiles
+        File referenceAnnotation
+        String? outputDir
+        String outPrefix = "gffcmp" # gffcmp is the default used by the program as well. This needs to be
+        # defined in order for the output values to be consistent and correct.
+        File? genomeSequences
+        Int? maxDistanceFreeEndsTerminalExons
+        Int? maxDistanceGroupingTranscriptStartSites
+        String? namePrefix
+        Boolean C = false
+        Boolean A = false
+        Boolean X = false
+        Boolean K = false
+        Boolean snCorrection = false
+        Boolean precisionCorrection = false
+        Boolean discardSingleExonTransfragsAndReferenceTranscripts = false
+        Boolean discardSingleExonReferenceTranscripts = false
+        Boolean noTmap = false
+        Boolean verbose = false
+        Boolean debugMode = false
+        # This workaround only works in the input section.
+        # Issue addressed at https://github.com/openwdl/wdl/pull/263
+        File? noneFile # This is a wdl workaround. Please do not assign!
+    }
+    # This allows for the creation of output directories"
+    String dirPrefix= if defined(outputDir) then outputDir + "/" else ""
+    String totalPrefix = dirPrefix + outPrefix
+
+
+    parameter_meta {}
+
+    command {
+        set -e
+        ~{preCommand}
+        ~{"mkdir -p " + outputDir}
+        gffcompare \
+        -r ~{referenceAnnotation} \
+        ~{"-o '" + totalPrefix + "'"} \
+        ~{"-s " + genomeSequences} \
+        ~{"-e " + maxDistanceFreeEndsTerminalExons} \
+        ~{"-d " + maxDistanceGroupingTranscriptStartSites} \
+        ~{"-p " + namePrefix} \
+        ~{true="-C" false="" C} \
+        ~{true="-A" false="" A} \
+        ~{true="-X" false="" X} \
+        ~{true="-K" false="" K} \
+        ~{true="-R" false="" snCorrection} \
+        ~{true="-Q" false="" precisionCorrection} \
+        ~{true="-M" false="" discardSingleExonTransfragsAndReferenceTranscripts} \
+        ~{true="-N" false="" discardSingleExonReferenceTranscripts} \
+        ~{true="-T" false="" noTmap} \
+        ~{true="-V" false="" verbose} \
+        ~{true="D" false="" debugMode} \
+        ~{"-i " + inputGtfList} \
+        ~{sep=" " inputGtfFiles}
+    }
+
+    # Output of gffcompare is not stable. It depends on the number of files in the input.
+    Int noFilesGtfList = if defined(inputGtfList) then length(read_lines(select_first([inputGtfList]))) else 0
+    Int noInputFiles = length(inputGtfFiles)
+    Boolean oneFile = (noFilesGtfList + noInputFiles) == 1
+    String annotatedName = if oneFile then "annotated" else "combined"
+
+    # Check if a redundant .gtf will be created
+    Boolean createRedundant = C || A || X
+
+    output {
+        File annotated = totalPrefix + "." + annotatedName + ".gtf"
+        File loci = totalPrefix + ".loci"
+        File stats = totalPrefix + ".stats"
+        File tracking = totalPrefix + ".tracking"
+        # noneFile is not stable. Please replace this as soon as wdl spec allows
+        File? redundant = if createRedundant then totalPrefix + ".redundant.gtf" else noneFile
+        File? missedIntrons = if debugMode then totalPrefix + ".missed_introns.gtf" else noneFile
+    }
+}
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