change runtime attrs to args #8413
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meganshand
suggested changes
Jul 11, 2023
| # runtime | ||
| String? gatk_docker_override | ||
| Int? mem |
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I think the mem, command_mem, and machine_mem arguments for this task were already hooked up correctly. Since mem was an optional input you could override the memory for this task and the java command appropriately the way it was set up before.
| @@ -275,7 +277,7 @@ task RevertSam { | |||
| } | |||
| runtime { | |||
| disks: "local-disk " + disk_size + " HDD" | |||
| memory: machine_mem + " MB" | |||
| memory: mem + " MB" | |||
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You can leave this as machine_mem so that you don't have to add the Int mem = machine_mem line. machine_mem is already overrideable. Or if you want to make it clearer to the user/more consistent with other tasks you can just rename machine_mem to mem without making an additional variable.
dyeramosu
commented
Jul 11, 2023
| } | ||
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| String output_vcf = "raw" + if compress then ".vcf.gz" else ".vcf" | ||
| String output_vcf_index = output_vcf + if compress then ".tbi" else ".idx" | ||
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| # Mem is in units of GB but our command and memory runtime values are in MB | ||
| Int machine_mem = if defined(mem) then mem * 1000 else 3500 | ||
| Int command_mem = machine_mem - 500 |
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@meganshand pushed new changes, let me know how this looks!
meganshand
approved these changes
Jul 11, 2023
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