BCCDC-PHL/symlink-seqs

Symlink all samples on a run when a run ID is supplied with no sample IDs file

dfornika opened this issue · 0 comments

When a --run-id is supplied with no --ids-file, we get this error:

Traceback (most recent call last):
  File "symlink-seqs", line 618, in <module>
    main(args)
  File "symlink-seqs", line 577, in main
    sample_ids = parse_ids_file(args.ids_file)
  File "symlink-seqs", line 404, in parse_ids_file
    with open(ids_file_path, 'r') as f:
TypeError: expected str, bytes or os.PathLike object, not NoneType

We should support a mode where all samples on a run are symlinked when a run ID is supplied with no sample IDs file.