align_make_input.sh now checks the extraction of flowcell and lane, and assigns 'unknown' if reads appear to be SRA origin where flowcell and lane are no longer in the read ID
Adds 'dos2unix' command for the config as a just in case
Added note to README to check the regexes in align_make_input.sh for filepath and flowcell/lane extraction
align_make_input.shnow checks the extraction of flowcell and lane, and assigns 'unknown' if reads appear to be SRA origin where flowcell and lane are no longer in the read IDalign_make_input.shfor filepath and flowcell/lane extraction