InitialWorkDirRequirement copies or symlinks files?

Question

[ionox0]

For InitialWorkDirRequirement, do the files get copied to the current directory or symlinked?

It seems that they are symlinked.

The reason that I have this question is because I would like to use glob: . and reference these InitialWorkDir files in a later step. However it seems that the the links become broken for these files once the step has finished and the next step has begun, and my assumption is that the directory that they came from gets deleted (at least when using the Toil runner implementation, I'm not experiencing this issue just running cwltool on its own).

Perhaps this is not a suitable method for referencing these files in later steps?

[drkennetz]

for cwltool they get symlinked not copied.

[dkennetz@node stg8786d387-abba-4fa8-ab23-29b3e941719b]$ pwd /tmp/tmpm05kw54z/stg8786d387-abba-4fa8-ab23-29b3e941719b $ls -alh lrwxrwxrwx 1 dkennetz 128 Jun 26 13:22 fastq.fastq.gz -> /path/to/fastq/input/fastq,fastq.gz

Answer 1

[ionox0]

Thank you @mr-c for the answer, which is also in the CWL spec:

If writable is false, the file may be made available using a bind mount or file system link to avoid unnecessary copying of the input file.