Snakefile 989 Bytes
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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)