List of to do for converting over to NF

[jennahamlin]

Description of feature

Below is a list of things which need to get completed. This is not an exhaustive list but based on what I can anticipate for now.

• [x] Need to get Python and Mash to be included when running the pipeline. Mash Dist is included in the nf-core modules but it isn't recognized. Currently must module load python and mash on cluster
• [x] When I gunzip files, filenames are converted to generic (read 1 and read 2) and does not maintain unique read id's. These should be the unique file name so that you know which results match to with isolate
• [x] Need to append Results and Run.log together and provide one file for each in the results output directory
• [x] Make sure email and template work
• [x] Remove any extra bits of code that is unnecessary from the template
• [x] Make test-data available for usage

[jennahamlin]

Below is a list of things which need to get completed. This is not an exhaustive list but based on what I can anticipate for now.

• [ ] Remove any extra bits of code that is unnecessary from the template - double check
• [ ] Add four more Legionella subset data to test dataset
• [x] Add option from NCBI datasets (--assembly-level) to bash script and nextflow parameters
• [ ] Perform liniting