Commit a959cec8 authored by Kenzo-Hugo Hillion's avatar Kenzo-Hugo Hillion
Browse files

Start rules for annotation with eggnogmapper2

parent 22379bcc
__eggnogmapper2_exec_command = config.get('eggnogmapper2', {}).get('exec_command', 'emapper.py')
__eggnogmapper2_annotate_options = config.get('eggnogmapper2', {}).get('annotate', {}).get('options', '')
__eggnogmapper2_annotate_threads = config.get('eggnogmapper2', {}).get('annotate', {}).get('threads', 4)
rule eggnogmapper2_annotate:
"""
Run annotate mode of eggnogmapper v2
"""
input:
__eggnogmapper2_annotate_input
output:
__eggnogmapper2_annotate_output
params:
exec_command = __eggnogmapper2_exec_command + ' --annotate_hits_table',
output_prefix = __eggnogmapper2_annotate_output_prefix,
options = __eggnogmapper2_annotate_options
threads:
__eggnogmapper2_annotate_threads
shell:
"""
{params.exec_command} {input} {params.options} --cpu {threads} -o {params.output_prefix}
"""
configfile: "config.yaml"
# ==== Snakefile path ====
__eggnogmapper2_annotate_rules = config.get("snakefiles", {}).get("eggnogmapper2_annotate")
__main_output_dir = config.get('output_dir', 'output')
# ==== Main config ====
SAMPLES = config.get('samples')
__input_dir = config.get('input_dir', 'data')
# ==== EggNOGmapper2 Annotate ====
__eggnogmapper2_output_dir = __main_output_dir + "/eggnogmapper2"
__eggnogmapper2_annotate_output_dir = __eggnogmapper2_output_dir + "/annotate"
__eggnogmapper2_annotate_input = "{dir}/{{sample}}.emapper.seed_orthologs".format(dir=__input_dir)
__eggnogmapper2_annotate_output_prefix = "{dir}/{{sample}}".format(dir=__eggnogmapper2_annotate_output_dir)
__eggnogmapper2_annotate_output = "{dir}/{{sample}}.emapper.annotations".format(dir=__eggnogmapper2_annotate_output_dir)
include: __eggnogmapper2_annotate_rules
rule all:
input: expand("{dir}/{{sample}}.emapper.annotations".format(dir=__eggnogmapper2_annotate_output_dir), sample=SAMPLES)
snakefiles:
eggnogmapper2_annotate: /pasteur/projets/policy01/Atm/snakemake/tools/eggnogmapper2/annotate/Snakefile
input_dir: /pasteur/projets/policy01/Atm/kenzo/sandbox/20200210_test_snakemake/test_output/eggnogmapper2/diamond/
output_dir: /pasteur/projets/policy01/Atm/kenzo/sandbox/20200210_test_snakemake/test_output
samples:
- all
eggnogmapper2:
exec_command: "/pasteur/homes/kehillio/venv/eggnog-mapper-v2/bin/python /pasteur/homes/kehillio/tools/eggnog-mapper/emapper.py"
annotate:
options: "--no_file_comments"
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