Merge pull request #222 from biowdl/BIOWDL-474

BIOWDL-474: Add new STAR options for processing rRNA depleted samples.

CHANGELOG.md

@@ -11,6 +11,8 @@ that users understand how the changes affect the new version.
 
 version 4.0.0-develop
 ---------------------------
++ STAR: Add options regarding alignment score (regarding read length as well)
+  for tweaking when processing rRNA depleted samples.
 + TALON: Update `minimumIdentity` to correct type (float, was integer)
   & set new default according to developers (0.8, was 0).
 + Added bcftools stats task.

star.wdl

@@ -95,6 +95,10 @@ task Star {
         String outFileNamePrefix
         String outSAMtype = "BAM SortedByCoordinate"
         String readFilesCommand = "zcat"
+        Int? outFilterScoreMin
+        Float? outFilterScoreMinOverLread
+        Int? outFilterMatchNmin
+        Float? outFilterMatchNminOverLread
         String? outStd
         String? twopassMode = "Basic"
         Array[String]? outSAMattrRGline
@@ -119,6 +123,10 @@ task Star {
         --genomeDir ~{sub(indexFiles[0], basename(indexFiles[0]), "")} \
         --outSAMtype ~{outSAMtype} \
         --readFilesCommand ~{readFilesCommand} \
+        ~{"--outFilterScoreMin " + outFilterScoreMin} \
+        ~{"--outFilterScoreMinOverLread " + outFilterScoreMinOverLread} \
+        ~{"--outFilterMatchNmin " + outFilterMatchNmin} \
+        ~{"--outFilterMatchNminOverLread " + outFilterMatchNminOverLread} \
         ~{"--outSAMunmapped " + outSAMunmapped} \
         ~{"--runThreadN " + runThreadN} \
         ~{"--outStd " + outStd} \
@@ -146,6 +154,10 @@ task Star {
         outFileNamePrefix: {description: "The prefix for the output files. May include directories.", category: "required"}
         outSAMtype: {description: "The type of alignment file to be produced. Currently only `BAM SortedByCoordinate` is supported.", category: "advanced"}
         readFilesCommand: {description: "Equivalent to star's `--readFilesCommand` option.", category: "advanced"}
+        outFilterScoreMin: {description: "Equivalent to star's `--outFilterScoreMin` option.", category: "advanced"}
+        outFilterScoreMinOverLread: {description: "Equivalent to star's `--outFilterScoreMinOverLread` option.", category: "advanced"}
+        outFilterMatchNmin: {description: "Equivalent to star's `--outFilterMatchNmin` option.", category: "advanced"}
+        outFilterMatchNminOverLread: {description: "Equivalent to star's `--outFilterMatchNminOverLread` option.", category: "advanced"}
         outStd: {description: "Equivalent to star's `--outStd` option.", category: "advanced"}
         twopassMode: {description: "Equivalent to star's `--twopassMode` option.", category: "advanced"}
         outSAMattrRGline: {description: "The readgroup lines for the fastq pairs given (in the same order as the fastq files).", category: "common"}
@@ -154,8 +166,7 @@ task Star {
         runThreadN: {description: "The number of threads to use.", category: "advanced"}
         memory: {description: "The amount of memory this job will use.", category: "advanced"}
         timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
+        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"}
     }
 }