Snakefile "ymp/rules/raxml.rules"

Env(name="raxml", base="bioconda", packages="raxml")

rule raxml_tree:
    message:
        "RAxML building tree from {input}"
    input:
        "{dir}/{file}.aligned.fastp.gz"
    output:
        "{dir}.raxml/{file}.tree"
    params:
        matrix="AUTO",
        algo="CAT",
        seed="12345",
        bs_seed="12345",
        bs_num="5",
    threads:
        32
    conda:
        "raxml"
    shell: """
    set -x
    x="`pwd`"
    cd {wildcards.dir}.raxml
    rm -rf {wildcards.file}/
    mkdir {wildcards.file}
    cd {wildcards.file}
    zcat "$x"/{input} > input.fasta

    raxmlHPC-PTHREADS-SSE3  \
      -f a \
      -m PROT{params.algo}{params.matrix} \
      -n {wildcards.file} \
      -T {threads} \
      -N {params.bs_num} \
      -p {params.seed} \
      -x {params.bs_seed} \
      -j  \
      -n out \
      -s input.fasta

    """