Open artur-baranowski-aa opened 3 weeks ago
Is there a workaround for this issue? I need to recognize files that have been stored on a shared network drive.
You need to specify it as a regular input file
For completeness, the NXF_FILE_ROOT
is a variable used by the nextflow runtime to resolve relative paths when using file
of channel.fromPath
. It's not meant to be used at task level.
Even more, a core nextflow pattern is to NOT used absolute path in the task script.
Closing this. Feel free to comment below if needed
Bug report
Unsure if I'm using this wrong, any help would be appreciated.
Expected behavior and actual behavior
According to the documentation and https://github.com/nextflow-io/nextflow/pull/3942, setting the
NXF_FILE_ROOT
variable should resolve some relative pathrelative_path
as${NXF_FILE_ROOT}/relative_path
.When running the workflow below, the files are generated in the specified directory under
${NXF_FILE_ROOT}
, but nextflow doesn't recognize them.Steps to reproduce the problem
Set some path prefix in the environment variable
NXF_FILE_ROOT
in the launching environment of Nextflow. Execute this minimal workflow:Program output
Files are present under
NXF_FILE_ROOT
, however nextflow does not recognize them:Environment