Merge branch 'master' into intervals_SplitNCigarReads

biopet.wdl

@@ -78,3 +78,60 @@ task SampleConfig {
         Object values = if (defined(tsvOutput) && size(tsvOutput) > 0) then read_map(tsvOutput) else { "": "" }
     }
 }
+
+task BaseCounter {
+    String? preCommand
+    String tool_jar #Should this be of type File?
+    File bam
+    File refFlat
+    String outputDir
+    String prefix
+
+    command {
+        set -e -o pipefail
+        ${preCommand}
+        mkdir -p ${outputDir}
+        java -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"
+    }
+}

htseq.wdl

+task HTSeqCount {
+    String? preCommand
+    Array[File] alignmentFiles
+    File gffFile
+    String outputTable
+    String? format
+    String? order
+    String? stranded
+
+    command {
+        set -e -o pipefail
+        ${preCommand}
+        htseq-count \
+        -f ${default="bam" format} \
+        -r ${default="pos" order} \
+        -s ${default="no" stranded} \
+        ${sep=" " alignmentFiles} \
+        ${gffFile} \
+        > ${outputTable}
+    }
+
+    output {
+        File counts = outputTable
+    }
+}
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mergecounts.wdl

+task MergeCounts {
+    String? preCommand
+
+    Array[File] inputFiles
+    String outputFile
+    String idVar
+    String measurementVar
+
+    # Based on a script by Szymon Kielbasa/Ioannis Moustakas
+    command <<<
+        set -e -o pipefail
+        ${preCommand}
+        R --no-save --slave <<CODE > ${outputFile}
+            library(dplyr)
+            library(reshape2)
+
+            listOfFiles <- c("${sep='", "' inputFiles}")
+
+            d <- do.call(rbind, lapply(listOfFiles, function(file){
+                d <- read.table(file, header=TRUE, comment.char="#")
+                colI <- grep(${measurementVar}, colnames(d))
+                colnames(d)[colI] <- strsplit(file, "/")[[1]][3]
+                d <- d %>% melt(id.vars=${idVar}, measure.vars=colI,
+                    variable.name="sample", value.name="count")
+            }))
+
+            d <- d %>% dcast(paste0(${idVar}, " ~ sample"), value.var="count")
+            write.table(d, sep="\t", quote=FALSE, row.names=FALSE)
+        CODE
+    >>>
+
+    output {
+        File mergedCounts = outputFile
+    }
+}
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stringtie.wdl

+task Stringtie {
+    String? preCommand
+    File alignedReads
+    File? referenceGFF
+    Int? threads
+    String assembledTranscriptsFile
+    Boolean? firstStranded
+    Boolean? secondStranded
+    String? geneAbundanceFile
+
+    command {
+        set -e -o pipefail
+        ${preCommand}
+        stringtie \
+        ${"-p " + threads} \
+        ${"-G " + referenceGFF} \
+        ${true="--rf" false="" firstStranded} \
+        ${true="fr" false="" secondStranded} \
+        -o ${assembledTranscriptsFile} \
+        ${"-A " + geneAbundanceFile} \
+        ${alignedReads} \
+
+    }
+
+    output {
+        File assembledTranscripts = assembledTranscriptsFile
+        File? geneAbundance = geneAbundanceFile
+    }
+
+    runtime {
+        threads: threads
+    }
+}
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