I run a task indicating a relative path for the stdout output, such as:
outputs: my_output_file: type: stdout stdout: parentdir/myfile.txt
So while the output is fine in the temporary directory, when using
cwltool --outdir /my/outputdir I am left with only
/my/outputdir/myfile.txt instead of the expected
So how is it possible to preserve the relative file hierarchy indicated in a tool stdout ? I would have thought that copying the root
cache dir to the root
outdir was the default. Any help and suggestion would be great.