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Commit b5d6e71a authored by Ruben Vorderman's avatar Ruben Vorderman
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Add outputBAMcompression to STAR

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......@@ -11,6 +11,8 @@ that users understand how the changes affect the new version.
version 4.0.0-develop
---------------------------
+ Alignment tasks (STAR, Hisat2, BWA) now produce BAM files at level 1
compression.
+ Hisat2 task has added controls for samtools.
+ Alignment tasks no longer produce BAM indexes as these are not needed
by the markduplicates step.
......
......@@ -103,6 +103,7 @@ task Star {
String? twopassMode = "Basic"
Array[String]? outSAMattrRGline
String? outSAMunmapped = "Within KeepPairs"
Int outBAMcompression = 1
Int? limitBAMsortRAM
Int runThreadN = 4
......@@ -129,6 +130,7 @@ task Star {
--outFileNamePrefix ~{outFileNamePrefix} \
--genomeDir ~{sub(indexFiles[0], basename(indexFiles[0]), "")} \
--outSAMtype ~{outSAMtype} \
--outBAMcompression ~{outBAMcompression} \
--readFilesCommand ~{readFilesCommand} \
~{"--outFilterScoreMin " + outFilterScoreMin} \
~{"--outFilterScoreMinOverLread " + outFilterScoreMinOverLread} \
......@@ -172,6 +174,7 @@ task Star {
limitBAMsortRAM: {description: "Equivalent to star's `--limitBAMsortRAM` option.", category: "advanced"}
runThreadN: {description: "The number of threads to use.", category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
outBAMcompression: {description: "The compression level of the output BAM.", 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"}
}
......
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