DOIAbstract
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...
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