How can I verify that a WDL workflow previously compiled with dxCompiler was compiled with the -streamFiles flag? Former User of DNAx Community_98 14 March 2023 00:00 3 comments I don't see any indication of streaming when I run `dx describe --verbose --json ` or `dx describe --verbose --json `, and I want to make sure that this worked. I was expecting to see something, possibly in the "inputeSpec" section of the json. Comments 3 comments Sort by Date Votes Ondrej Klempir DNAnexus Team 15 March 2023 20:14 I was super interested to know how to do this! So I consulted this with DNAnexus dxCompiler experts and this is their answer (I like it!): In a job log look for the following line:java -jar /dxExecutorWdl.jar task run /home/dnanexus -traceLevel 1 -streamFiles PerFile -streamFiles is not a flag it's an argument and it has values [all, none, perfile], see docstring: -streamFiles [all,none,perfile] Whether to mount all files with dxfuse (do not use the download agent), to mount no files with dxfuse (only use download agent), or to respect the per-file settings in WDL parameter_meta sections (default). 0 Former User of DNAx Community_98 15 March 2023 20:16 Thank you for the answer! How did you reach out to the DNAnexus dxCompiler experts? (In case I need to in the future) 0 Ondrej Klempir DNAnexus Team 15 March 2023 20:34 You can contact ukbiobank-support@dnanexus.com. 0 Please sign in to leave a comment.
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I was super interested to know how to do this! So I consulted this with DNAnexus dxCompiler experts and this is their answer (I like it!):
In a job log look for the following line:
java -jar /dxExecutorWdl.jar task run /home/dnanexus -traceLevel 1 -streamFiles PerFile
-streamFiles is not a flag it's an argument and it has values [all, none, perfile], see docstring:
-streamFiles [all,none,perfile]
Whether to mount all files with dxfuse (do not use the
download agent), to mount no files with dxfuse (only use
download agent), or to respect the per-file settings in WDL
parameter_meta sections (default).
Thank you for the answer!
How did you reach out to the DNAnexus dxCompiler experts? (In case I need to in the future)
You can contact ukbiobank-support@dnanexus.com.
Please sign in to leave a comment.