Currently docs/_writing_parameters.rst uses this as a boolean parameter example:
-V shift quality by '(-Q) - 33'
This seems inappropriate and rather than exposing it as a user setting it should be automatic conditional on the datatype (i.e. use this for fastqillumina only). This could be used in a more complex example using conditionals in the Cheetah command tag and multiple input types.
I would suggest we replace the boolean parameter -V example with something simpler like -C or -N:
-C drop comments at the header lines
-N drop sequences containing ambiguous bases
Currently
docs/_writing_parameters.rst
uses this as a boolean parameter example:This seems inappropriate and rather than exposing it as a user setting it should be automatic conditional on the datatype (i.e. use this for
fastqillumina
only). This could be used in a more complex example using conditionals in the Cheetah command tag and multiple input types.I would suggest we replace the boolean parameter
-V
example with something simpler like-C
or-N
: