NorwegianVeterinaryInstitute/ALPPACA: v2.0.0

Major update following the JOSS review of ALPPACA. The pipeline has been changed to partially reflect the structure of NF-core pipelines. The following changes have been made:

• Pipeline is now executed directly using nextflow run, locally and directly from github
• Parameters are now supplied in the run command. Default parameter values are given in the nextflow.config
• Input changed to csv file containing the paths and sample names. The bin/generate_input.R script have been added to make it easy for users to generate this file
• Pipeline can be run by using singularity, docker, or conda as container handlers
• Example configuration files are supplied
• The pipeline now has test functionality, use with the test profile
• Added yml files for creating a run environment for the pipeline
• Updates to the wiki on how to run and configuration settings etc. to reflect the changes described above