Followed naming convention as established by Hjolli & streamlined output naming etc. accordingly.
rDNA filtering occurs only when blacklist is provided (emulates VCF behavior). Additional tests to ensure file paths exist and dependencies are present. Fully compatible with paired end data now including automated finding of the shortest common denominator in the paired end fastq file names. Use of an associative array to log parameters and print them in a formatted manner into the log-file. Logged all names of generated files in the parameters.log file.
Followed naming convention as established by Hjolli & streamlined output naming etc. accordingly.
rDNA filtering occurs only when blacklist is provided (emulates VCF behavior). Additional tests to ensure file paths exist and dependencies are present. Fully compatible with paired end data now including automated finding of the shortest common denominator in the paired end fastq file names. Use of an associative array to log parameters and print them in a formatted manner into the log-file. Logged all names of generated files in the parameters.log file.