---
global:
    - ROOT: data/raw
    - indir: data/raw
    - outdir: data/processed
    - file_rule: (.vcf)$|(.vcf.gz)$
rules:
    - bgzip:
        process: |
            {
                if(! -f "$self->{indir}/$sample.vcf.gz"){
                    $OUT .= "bgzip $self->{indir}/$sample.vcf && tabix $self->{indir}/$sample.vcf.gz\n";
                }

            }
    - normalize_snpeff:
        local:
            - indir: "{$self->ROOT}"
        process: |
            bcftools view {$self->indir}/{$sample}.vcf.gz | sed 's/ID=AD,Number=./ID=AD,Number=R/' \
                | vt decompose -s - \
                | vt normalize -r $REFGENOME - \
                | java -Xmx4G -jar $SNPEFF/snpEff.jar -c \$SNPEFF/snpEff.config -formatEff -classic GRCh37.75  \
                | bgzip -c > \
                {$self->{outdir}}/{$sample}.norm.snpeff.gz && tabix {$self->{outdir}}/{$sample}.norm.snpeff.gz
    - gemini_sqlite:
        process: |
            gemini load -v {$self->indir}/{$sample}.norm.snpeff.gz \
                --skip-cadd -t snpEff \
               {$self->outdir}/{$sample}.vcf.db