Advanced: Adding unsupported assemblers

Adding new assemblers

In order to add a new assembler to the pipeline that is not presently included, three things need to be included:

1. A rule for the assembler, including a command that can be run using software in the specified conda environment, called <assembler>.
2. A rule to “clean” the assembly output, named <assembler>_clean, including moving the completed assemblies to the shared assembly folder, specified as assembledDIR, which is a subdirectory of the outputDIR, also specified in the configuration file. Intermediate files should also be moved to a scratch directory or deleted, based on user preferences and space requirements. Any other files needed by other tools or desired by the user should be moved to a subdirectory of the output directory. If they are specified as output files, snakemake will generate them automatically. Otherwise, the user will need to manually create directories that do not already exist (specifying them as output files is more extensible).
3. A list entry for the assembler in the configuration file that matches the name of <assembler> in each snakemake rule.