ValueError: No objects to concatenate

[linzhi2013]

Hi Tobias,

When SEQCAP tries to locate the sample folders at the very beginning (see the assemble_reads.py file and below codes)

def main(args):
    input_folder = args.input
    cores = args.cores
    subfolder_list = [subfolder for subfolder, __, __ in os.walk(input_folder) if os.path.basename(subfolder) != os.path.basename(input_folder)]

The os.walk() does not work for symbolic links, so the subfolder_list is empty, which then raises the following error:

There are several reasons for using symbolic links in the input_folder for the sample directories:

1. In my case, I have 97 samples, and SEQCAP always failed when it just finished 81 samples. Therefore, I would like to link the fastq files of unfinished samples into a new directory, but the os.walk() does not work for symbolic links.

2. When the users already have decompressed fastq files with different naming formats, it makes sense if the users can just create an input_folder and link these fastq files into this folder while renaming the fastq files at the same time.

The solution is simple, just change the code into:

os.walk(input_folder, followlinks=True)

But maybe you have some reasons not to do so?

Thanks!

Guanliang