Closed johnbradley closed 3 years ago
I think the 5. Create a dictionary file for using picard tools
step in Escape_Variants.md is also a one time step.
The picard CreateSequenceDictionary
fails if run more than once with an error like:
...MT246667.dict already exists. Delete this file and try again, or specify a different output file.
Yes @johnbradley, this step should be run only once. It shows an error if the dict file is already there.
To fix this I was thinking about adding another top level script and moving all the one-time steps there. Something like:
./setup-escape-variants.sh
This would consist of the two one-time steps from Escape_Variants.md.
@wodanaz How does that sound?
I like the sound of this
As mentioned in comment https://github.com/wodanaz/Assembling_viruses/pull/1#issuecomment-774093979 some steps only need to be run once. In this case the reference genome only needs to be indexed once. Currently we index the genome every time.