correct barcode instructions in readmes

For some reason tr '\r' '\n' < $i >$i doesn't work and files became
blank, better to correct from text editor
fixed barcodes

when I originally tried tr to change the line endings the content of
the files got lost. I therefore saved manually with line break LF.
Replace everywhere.
create chetsheet with common commands
ignore changes to cheatsheet
modify paths to run from special scratch area and run

Because of the second read pair that needs to be faked in order to the
pipeline to work the input data gets to large and I will exceed my
scratch area limit. Leo from Grace team asked me to use a temporarly
special place to run analysis
change paths to write all to newgpfs

files in tmp folder were to much for home, I was adviced to Leo to run
all from newgpfs
corrected paths

as expected first try never fucking works
get readme up to processing first look
demultiplex