Merge pull request #197 from biowdl/add_UMI_separator

Add umi separator

CHANGELOG.md

@@ -11,6 +11,7 @@ that users understand how the changes affect the new version.
 
 version 3.0.0
 ---------------------------
++ Add optional input umiSeparator in umi-tools dedup task.
 + Update command section syntax Minimap2, Talon, TranscriptClean and Centrifuge.
 + Add CCS workflow WDL files (ccs.wdl, lima.wdl, isoseq3.wdl).
 + Update TALON version to 4.4.2.

umi-tools.wdl

@@ -70,6 +70,7 @@ task Dedup {
     input {
         File inputBam
         File inputBamIndex
+        String? umiSeparator
         String outputBamPath
         String? statsPrefix
         Boolean paired = true
@@ -89,6 +90,7 @@ task Dedup {
         --stdin ~{inputBam} \
         --stdout ~{outputBamPath} \
         ~{"--output-stats " + statsPrefix} \
+        ~{"--umi-separator=" + umiSeparator}
         ~{true="--paired" false="" paired}
         samtools index ~{outputBamPath} ~{outputBamIndex}
     }
@@ -111,9 +113,10 @@ task Dedup {
         inputBamIndex: {description: "The index for the ipnut BAM file.", cateogry: "required"}
         outputBamPath: {description: "The location to write the output BAM file to.", category: "required"}
         statsPrefix: {description: "The prefix for the stats files.", category: "advanced"}
+        umiSeparator: {description: "Seperator used for UMIs in the read names.", category: "advanced"}
         paired: {description: "Whether or not the data is paired.", category: "common"}
         memory: {description: "The amount of memory required for the task.", category: "advanced"}
         dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
                       category: "advanced"}
     }
-}
\ No newline at end of file
+}