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MDU-PHL / bohra

A pipeline for bioinformatics analysis of bacterial genomes
GNU General Public License v3.0
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fail gracefully if files are not accessible #48

Closed kristyhoran closed 3 years ago

kristyhoran commented 3 years ago

If input files are not accessible:

  1. If reads are not present or no permissions fail before running workflow
  2. If prefill path not accessible for assembly and speciation default to running assembly or speciation
kristyhoran commented 3 years ago

https://docs.python.org/3/library/os.html#os-file-dir

kristyhoran commented 3 years ago

Use os.access(path, os.R_OK) since files only need to be readable - no modifications need be made.

kristyhoran commented 3 years ago

fixed with commit 9723c51