inflexible bbduk trim make input script

[georgiesamaha]

trim script expects a specific fastq naming convention that makes it incompatible with sequence data from Ramaciotti centre. To customise, will need to edit basename variable definition (see lines 80-83):

For example, to accept fqs ending in _R1/2_001.fastq.gz:

basename=$(basename "$fastq" | sed -E 's/_[R][12]_001\.fastq\.gz$//')
		paired_extension="${fastq#*.}"
		uniq_basename="${basename}"
		which_pair=$(basename "$fastq" | sed -E 's/^.*_([R][12])_001\.fastq\.gz$/\1/')