Better handle one time steps

[johnbradley]

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.

[johnbradley]

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.

[wodanaz]

Yes @johnbradley, this step should be run only once. It shows an error if the dict file is already there.

[johnbradley]

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.

• 1 Index Genome Reference - index-reference-genome.sh
• 5 Create a dictionary file for using picard tools - create-picard-dictionary.sh

@wodanaz How does that sound?

[wodanaz]

I like the sound of this