execution.yaml

#-----------Execution modules for RIMA-------------#
#--------------Environment module for first time users-------------#
#Note: This module creates the enviornment necessary to run the remaining modules. Installation required only for first time on any server. For recurring users, the command can be set to false to avoid reinstallations.
environment: false

#------------Pipeline modules for RNA data--------------------#
#Note: Preprocess individual and cohort module necessary to get the alignment and quality results. Run the remaining modules only after these two modules.
preprocess_individual_step1: true
preprocess_individual: true
mutation_individual: true
immune_response_individual: true
immune_repertoire_individual: true
neoantigen_individual: true
microbiome_individual: true