rule filter:
    input:
        sequences = "data/sequences.fasta",
        metadata = "data/metadata.tsv"
    output:
        sequences = "results/filtered.fasta"
    params:
        min_date = 2012
    shell:
        """
        augur filter \
            --sequences {input.sequences} \
            --metadata {input.metadata} \
            --output {output.sequences} \
            --min-date {params.min_date}
        """

rule align:
    input:
        sequences = rules.filter.output.sequences,
    output:
        alignment = "results/aligned.fasta"
    shell:
        """
        augur align \
            --sequences {input.sequences} \
            --output {output.alignment}
        """