Commit d57802de authored by Kenzo-Hugo Hillion's avatar Kenzo-Hugo Hillion
Browse files

add rule for diamond through eggnogmapper2

parent ddb68576
__eggnogmapper2_exec_command = config.get('eggnogmapper2', {}).get('exec_command', 'emapper.py')
__eggnogmapper2_diamond_options = config.get('eggnogmapper2', {}).get('diamond', {}).get('options', '')
__eggnogmapper2_diamond_threads = config.get('eggnogmapper2', {}).get('diamond', {}).get('threads', 4)
rule eggnogmapper2_diamond:
"""
Run diamond mode of eggnogmapper v2
"""
input:
__eggnogmapper2_diamond_input
output:
__eggnogmapper2_diamond_output
params:
exec_command = __eggnogmapper2_exec_command + ' -m diamond',
output_prefix = __eggnogmapper2_diamond_output_prefix,
options = __eggnogmapper2_diamond_options
threads:
__eggnogmapper2_diamond_threads
shell:
"""
{params.exec_command} {params.options} --cpu {threads} -i {input} -o {params.output_prefix}
"""
configfile: "config.yaml"
# ==== Snakefile path ====
__eggnogmapper2_diamond_rules = config.get("snakefiles", {}).get("eggnogmapper2_diamond")
__main_output_dir = config.get('output_dir', 'output')
# ==== Main config ====
SAMPLES = config.get('samples')
__input_dir = config.get('input_dir', 'data')
# ==== EggNOGmapper2 Diamond ====
__eggnogmapper2_output_dir = __main_output_dir + "/eggnogmapper2"
__eggnogmapper2_diamond_output_dir = __eggnogmapper2_output_dir + "/diamond"
__eggnogmapper2_diamond_input = "{dir}/{{sample}}.fa".format(dir=__input_dir)
__eggnogmapper2_diamond_output_prefix = "{dir}/{{sample}}".format(dir=__eggnogmapper2_diamond_output_dir)
__eggnogmapper2_diamond_output = "{dir}/{{sample}}.emapper.seed_orthologs".format(dir=__eggnogmapper2_diamond_output_dir)
include: __eggnogmapper2_diamond_rules
rule all:
input: expand("{dir}/{{sample}}.emapper.seed_orthologs".format(dir=__eggnogmapper2_diamond_output_dir), sample=SAMPLES)
snakefiles:
eggnogmapper2_diamond: /pasteur/projets/policy01/Atm/snakemake/tools/eggnogmapper2/diamond/Snakefile
input_dir: /pasteur/projets/policy01/Atm/kenzo/sandbox/20200210_test_snakemake/test_output/split_fasta
output_dir: /pasteur/projets/policy01/Atm/kenzo/sandbox/20200210_test_snakemake/test_output
samples:
- test_00000
- test_00001
- test_00002
eggnogmapper2:
exec_command: "/pasteur/homes/kehillio/venv/eggnog-mapper-v2/bin/python /pasteur/homes/kehillio/tools/eggnog-mapper/emapper.py"
diamond:
options: "--no_annot --no_file_comments"
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