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Metagenomics
snakemake
Commits
d57802de
Commit
d57802de
authored
Mar 13, 2020
by
Kenzo-Hugo Hillion
♻
Browse files
add rule for diamond through eggnogmapper2
parent
ddb68576
Changes
3
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tools/eggnogmapper2/diamond/Snakefile
0 → 100644
View file @
d57802de
__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}
"""
tools/eggnogmapper2/diamond/example_usage/Snakefile
0 → 100644
View file @
d57802de
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)
tools/eggnogmapper2/diamond/example_usage/config.yaml
0 → 100644
View file @
d57802de
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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