# minimal example
configfile: "../snakemake/config.yaml"
import os
rule generateInclude: 
    input: 
        archaic_inc=config['input']['archaic_include'], 
        modern_inc=config['input']['modern_include']
    output: 
        all_include='include_{reference_genome}.bed'
    params:     
        reference_genome='{reference_genome}'
    shell: 
        """
        if [ {params.reference_genome}=='hg19' ]; then
            bedtools intersect -a <(zcat {input.archaic_inc} | sed 's/^chr//') \
                -b <(zcat {input.modern_inc} | sed 's/^chr//') > {output.all_include}
        else
            bedtools intersect -a <(zcat {input.archaic_inc}) \
                -b <(zcat {input.modern_inc}) > {output.all_include}
        fi
        """
rule all: 
    input: 
        'include_hg19.bed'

Target rules may not contain wildcards. Please specify concrete files or a rule without wildcards.

rule all: 
    input: 
        'include_hg19.bed'
rule generateInclude:
    ...