pathvar in rule all

**Describe the bug**
rule all in the template is missing the `pathvar`

```snakemake
rule all:
    message:
        "ERROR: Invalid `rule all:` call"
    default_target: True
    output:
        "INVALID",
    log:
        stderr="<logs>/all.stderr",  # Here
    conda:
        "envs/shell.yaml"
    shell:
        'echo "This workflow must be called as a snakemake module." > {log.stderr}'

```
