Staging input files in a subfolder changes their names when they are symlinks

[mfoll]

When input files are symlinks (like titi.txt in the following example) pointing to a file with a different name (tata.txt in the example) AND we ask nextflow to stage this file as an input in a subfolder (TXT/ here), the new link created by nextflow in this folder in work is renamed with the name of the symlink target (tata.txt here).
Here is a replicable toy example of the bug. My current environment:

[follm@hn test_nf]$ ls -l
total 0
lrwxrwxrwx 1 follm lsu 20 Feb 22 17:08 titi.txt -> /data/follm/tata.txt
-rw-r--r-- 1 follm lsu  0 Feb 22 17:07 toto.txt

Note here titi.txt -> /data/follm/tata.txt. The nextflow script causing the bug:

txt = Channel.fromPath( '*.txt' ).toList()

process printHello {

   input:
   file 'TXT/*' from txt  

   output: 
   stdout into result

   shell:
   '''
   ls -l *
   '''
}	

result.println()

The output when running the script:

[follm@hn test_nf]$ nextflow run ~/nf_scripts/test.nf 
N E X T F L O W  ~  version 0.23.3
Launching `/home/follm/nf_scripts/test.nf` [grave_pike] - revision: a5b30c5813
[warm up] executor > lsf
[97/3b9225] Submitted process > printHello (1)
total 0
lrwxrwxrwx 1 follm lsu 26 Feb 23 09:47 tata.txt -> /mnt/beegfs/follm/tata.txt
lrwxrwxrwx 1 follm lsu 34 Feb 23 09:47 toto.txt -> /mnt/beegfs/follm/test_nf/toto.txt

Note that here tata.txt -> /mnt/beegfs/follm/tata.txt while the file was originally named titi.txt (note that in my system /data -> /mnt/beegfs, so this is correctly resolved).

Simply changing file 'TXT/*' from txt to file txt or even file '*' from txt returns the correct output (at least what I am expecting...):

[follm@hn test_nf]$ nextflow run ~/nf_scripts/test.nf 
N E X T F L O W  ~  version 0.23.3
Launching `/home/follm/nf_scripts/test.nf` [gloomy_noether] - revision: 31557eca14
[warm up] executor > lsf
[95/be833c] Submitted process > printHello (1)
lrwxrwxrwx 1 follm lsu 26 Feb 23 10:02 titi.txt -> /mnt/beegfs/follm/tata.txt
lrwxrwxrwx 1 follm lsu 34 Feb 23 10:02 toto.txt -> /mnt/beegfs/follm/test_nf/toto.txt

Note here titi.txt -> /mnt/beegfs/follm/tata.txt.

[mfoll]

It seems to be related to #222, as the output is correct with a version before this has been fixed (but symlinks are not resolved of course):

[follm@hn test_nf]$ export NXF_VER=0.22.0
[follm@hn test_nf]$ nextflow run ~/nf_scripts/test.nf 
N E X T F L O W  ~  version 0.22.0
Launching `/home/follm/nf_scripts/test.nf` [lonely_mahavira] - revision: a5b30c5813
[warm up] executor > lsf
[6c/baf532] Submitted process > printHello (1)
total 0
lrwxrwxrwx 1 follm lsu 34 Feb 23 10:09 titi.txt -> /mnt/beegfs/follm/test_nf/titi.txt
lrwxrwxrwx 1 follm lsu 34 Feb 23 10:09 toto.txt -> /mnt/beegfs/follm/test_nf/toto.txt

[pditommaso]

Good shot! I've just uploaded 0.23.4-SNAPSHOT, please confirm that fixes the issue on your side.

[mfoll]

I just checked and it is working as expected. Thanks for the quick fix!

[pditommaso]

Released with version 0.23.4