Could run FASTQC on the input reads, and do some simple quality checking (e.g. cat the .html and see if there are files where the per sequence quality is failed -> indicated a bad sequencing run), and error out if bad quality is found. This would prevent the user from using the pipeline inadvertently with very bad sequencing data.
Could run FASTQC on the input reads, and do some simple quality checking (e.g. cat the .html and see if there are files where the per sequence quality is failed -> indicated a bad sequencing run), and error out if bad quality is found. This would prevent the user from using the pipeline inadvertently with very bad sequencing data.
Also see https://github.com/transXpress/transXpress-snakemake/issues/5