You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
I am not sure this is a real "issue", so I opened a discussion instead of reporting it as such.
Basically, it is as the title says: in processes that are run inside a Docker container, Nextflow fails to publish output files if the publishDir directive is set to "link". The underlying reason seems to be that the default umask on most Linux systems is 0022, which does not allow other users to modify that file. Since files generated via Docker are owned by a user that has a different UID as the host (as discussed in #1295), hard links cannot be created.
A workaround I've used is to modify the Docker container to create files with umask 0000, but I wonder if Nextflow could handle this transparently to the user.
reacted with thumbs up emoji reacted with thumbs down emoji reacted with laugh emoji reacted with hooray emoji reacted with confused emoji reacted with heart emoji reacted with rocket emoji reacted with eyes emoji
-
I am not sure this is a real "issue", so I opened a discussion instead of reporting it as such.
Basically, it is as the title says: in processes that are run inside a Docker container, Nextflow fails to publish output files if the publishDir directive is set to "link". The underlying reason seems to be that the default umask on most Linux systems is
0022
, which does not allow other users to modify that file. Since files generated via Docker are owned by a user that has a different UID as the host (as discussed in #1295), hard links cannot be created.A workaround I've used is to modify the Docker container to create files with umask
0000
, but I wonder if Nextflow could handle this transparently to the user.Beta Was this translation helpful? Give feedback.
All reactions