Is your feature request related to a problem? Please describe.
Many new users to bioinf. do not consider at the beginning keeping their work in an organised fashion.
As EAGER produces a lot of intermediate files in work/ as well as large output files, we should assist making sure users keep their runs organised and tidy.
Therefore, we should make the --outdir and -w parameters more visible in both help documentation and help message, increasingly the likelihood of a user specifying exactly where the run output should go - particularly as we have so many parameters now, it'll take a long time for a users to get there and they miss it.
Is your feature request related to a problem? Please describe.
Many new users to bioinf. do not consider at the beginning keeping their work in an organised fashion.
As EAGER produces a lot of intermediate files in
work/as well as large output files, we should assist making sure users keep their runs organised and tidy.Therefore, we should make the
--outdirand-wparameters more visible in both help documentation and help message, increasingly the likelihood of a user specifying exactly where the run output should go - particularly as we have so many parameters now, it'll take a long time for a users to get there and they miss it.