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Localization problems with absolute path input

pdagostopdagosto Rockville, MDMember

I have the following simple workflow:

workflow variantCaller { 
   File rawReadsDir
   call changeDir {
       input: dir=rawReadsDir

task changeDir {
     File dir
    command {
       cd ${dir}

In my inputs file I specify an absolute path for rawReadsDir:

  "variantCaller.rawReadsDir": "/home/username/path_to_raw_reads_dir"

When I execute using the local back end the path I specified in my inputs has the path to the cromwell-executions directory pre-pended to it:


It snot clear to me why this is happening. Shouldn't the absolute path be respected as per the documentation?

I tried changing the root in the cromwell configuration file but this did not work either.

What's the secret to getting cromwell to accept and respect an absolute path as input?

Best Answer


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