File Options

indir outdir

The initial indir is where samples are found

All output is written relative to the outdir

INPUT OUTPUT

Special variables that can have input/output

coerce_abs_dir

Coerce dirs to absolute paths (True) Keep paths as relative directories (False)

create_outdir

Type Specific Process Directives

Sometimes you want a type specific way of processing directives. This will generally require two different methods

  process_directive*
  walk_directives*

process_directive gives some official parameters walk_directives walks the data structure

Take a look at the methods in 'BioX::Workflow::Command::run::Rules::Directives::Walk'

Your functions will probably be very similar

walk_directives_paths

Invoke with walk { wanted => sub { $self->directives(@_) } }, $self->other_thing;

Acts funny with $self->some_other_thing is not a reference