created variable for user to specify java heap size in picard #8406
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| @@ -25,6 +25,8 @@ workflow MitochondriaPipeline { | |||
| File? ref_fasta_index | |||
| File? ref_dict | |||
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| String java_heap_memory = "1000m" | |||
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I think this would be more convenient to declare only within the task itself. It will still show up as an optional input in Terra, but it means fewer overall inputs that you have to thread through the main wdl.
| @@ -247,6 +250,7 @@ task RevertSam { | |||
| input { | |||
| File input_bam | |||
| String basename = basename(input_bam, ".bam") | |||
| String heap_mem | |||
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I would tie this in to the memory declaration in the runtime arguments as well. That way if you want to increase the memory you'll increase the machine as well as the java argument. It's also good to leave some extra memory on the machine, so it would look like the following:
Int machine_mem = 2000
Then outside of the input block you'd have:
Int java_mem = machine_mem - 1000
Then you'd use it in the java command as:
java -Xmx~{java_mem}m -jar /usr/gitc/picard.jar \
And in the runtime block change the memory to the following:
memory: machine_mem + " MiB"
You could also change the unit here to GB if you want. Here's an example of what I'm trying to say here: https://github.com/broadinstitute/gatk/blob/master/scripts/cnn_variant_wdl/cnn_variant_common_tasks.wdl#L33
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@meganshand sounds good, thanks for the example! just pushed the new changes, let me know what you think. thanks!
due to error
Exception in thread "main" java.lang.OutOfMemoryError: Java heap space: failed reallocation of scalar replaced objectsduring RevertSam step in MitochondriaPipeline.wdl @meganshand