global-vs-local-variables.md

Global vs Local Variables

Variables are defined in two ways, globally and locally.

Global Variables

Global variables are defined at the top of your file can be accessed at any point in your workflow.

Here is an example of a common global variable declaration.

---
global:
  - sample_rule: Sample_.*
  - indir: data/raw
  - outdir: data/processed
  - find_sample_bydir: 1
  - by_sample_outdir: 1
  - root_dir: data

Local Variables

Local variables are declared per rule, and can only be accessed with in a rule. A local variable can override a global variable, but will only override it in that rule.

rules:
  ##This start the beginning of a rule.
  - qc:
      ##This starts the variable declaration
      local:
        - root_dir: 'data/analysis'
        - INPUT: '{$self->root_dir}/some_input_qc'
        - OUTPUT:
            - some_output_qc
      ##This is what we actually want to output
      process: |-
        INDIR: {$self->indir}
        INPUT: {$self->INPUT}
        outdir: {$self->outdir}
        OUTPUT: {$self->OUTPUT->[0]}

Notice that root_dir has been declared in the global and local rule. For the qc rule_ root_dir _would be evaluated as 'data/analysis' (with the full path name, of course), but throughout the workflow would be available as 'data'.