Snakefile "ymp/rules/align.rules"

rule combine_with_ref:
    message:
        "Adding {wildcards.gene} reference sequences to {input[1]}"
    input:
        "{gene}_ref.fastp",
        "{dir}/{query}.{gene}.e{evalue}.fastp"
    output:
        "{dir}/{query}.{gene}.e{evalue}.with_ref.fastp.gz"
    shell:
        "zcat {input} | gzip -c > {output}"

rule align_mafft:
    message:
        "MaFFT aligning {input}"
    input:
        "{dir}/{file}.fastp"
    output:
        "{dir}.mafft/{file}.aligned.fastp.gz"
    log:
        "{dir}.mafft/{file}.log"
    threads:
        32
    shell:"""
    cat {input} | \
    mafft \
      --maxiterate 1000 \
      --localpair \
      --reorder \
      --thread {threads} \
      - \
      2> {log} | gzip -c > {output}
    """