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
"""