How do I keep a glob from copying a file in Cromwell / WDL

Bioinformatics Asked on March 30, 2021

Using Crowell 52. When I do a glob to get matching files, Cromwell places a copy of each matching file in the glob-* directory.

As these are multi-gigabyte Bam files, I’d really prefer for Cromwell to store soft links to the files, rather than full copies.

The code:

   output {
      Array[File] Outputs = glob("*.fastq.gz")

Is it possible to make this happen?

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