input sequences endings

[d-j-e]

At the moment the pipe only takes Illumina paired-end with the endings _1.fastq.gz, _2.fastq.gz. This currently means the user has to rename the reads to match the pattern before running the pipe (same goes for IT reads and Illumina single end reads).

The pipe will be changed in two development stages - the first stage will require the user to enter the pattern for the reads if different to the default (default - current settings)

the second stage of development will be to get the pipe to work out the patterns used and apply them as needed...