add rule for diamond through eggnogmapper2

tools/eggnogmapper2/diamond/Snakefile

+__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

+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

+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"