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?

  • 1
    $\begingroup$ It would help your case to show the code you're using. $\endgroup$
    – Ram RS
    Mar 9, 2021 at 15:51
  • $\begingroup$ @RamRS added above $\endgroup$ Mar 10, 2021 at 15:12

1 Answer 1


As stated in https://github.com/broadinstitute/cromwell/issues/4395

The problem may be because you can't hardlink folders on your system for various reasons (i.e. filesystem doesn't allow hardlinking folders, only files, or you are trying to link between different filesystems).

You can try overriding the default way glob works.

i.e. add this to your cromwell.config

glob-link-command = "ls -L GLOB_PATTERN 2> /dev/null | xargs -I ? ln -s ? GLOB_DIRECTORY"

Like this

  default = "Slurm"
    Htcondor {
      actor-factory = "cromwell.backend.impl.sfs.config.ConfigBackendLifecycleActorFactory"

        glob-link-command = "find GLOB_PATTERN 2> /dev/null | xargs -I ? ln -s ? GLOB_DIRECTORY"

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