Error in prepare_files_for_report with single end only
I ran some samples, all single end, and got this error:
FileNotFoundError in line 1251 of /scicore/home/zavolan/burri0000/zavolab_projects/rnaseqpipeline/Snakefile:
[Errno 2] No such file or directory: 'results/paired_end'
File "/scicore/home/zavolan/burri0000/zavolab_projects/rnaseqpipeline/Snakefile", line 1251, in __rule_prepare_files_for_report
File "/scicore/home/zavolan/burri0000/miniconda3/envs/rnaseq_pipeline/lib/python3.6/shutil.py", line 471, in rmtree
File "/scicore/home/zavolan/burri0000/miniconda3/envs/rnaseq_pipeline/lib/python3.6/shutil.py", line 469, in rmtree
File "/scicore/home/zavolan/burri0000/miniconda3/envs/rnaseq_pipeline/lib/python3.6/concurrent/futures/thread.py", line 56, in run
the error seems to come from line 1251 in Snakefile. The snippet shows the complete call:
shutil.rmtree(
os.path.join(
params.results_dir,
"paired_end"),
ignore_errors=False,
onerror=None)
There is no directory paired_end. This shutil.rmtree() call should be expanded by the possibility that the directory does not exist or something similar. Similarly for the directory single_end.