Bug #12183
Updated by Peter Amstutz over 6 years ago
This is suspicious:
2017-08-28T11:09:17.982121623Z CMD: ln -s /var/spool/cwl/STAR-Fusion_outdir/star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.filtered /var/spool/cwl/STAR-Fusion_outdir/star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered
This seems to be creating a symlink to an absolute path inside the container. However, crunch-run (which collects the outputs) executes outside the container, which means it cannot dereference symlinks to arbitrary paths inside the container. It is already able to handle symlinks to mounted input files, and relative symlinks within the output directory, but doesn't correctly handle this case of a symlink with an absolute path to another file in the output directory. This should be handled correctly.