Commit 93eb643b authored by Kenzo-Hugo Hillion's avatar Kenzo-Hugo Hillion
Browse files

starting cat

parent d57802de
rule cat:
"""
Split a FASTA file with the desired number of sequences per chunk
"""
input:
__cat_input
output:
__cat_output
shell:
"""
cat {input} > {output}
"""
configfile: "config.yaml"
# ==== Snakefile path ====
__cat_rules = config.get("snakefiles", {}).get("cat")
__main_output_dir = config.get('output_dir', 'output')
# ==== Main config ====
SAMPLES = config.get('samples')
__input_dir = config.get('input_dir', 'data')
# ==== EggNOGmapper2 Diamond ====
__cat_merged_name = config.get('cat', {}).get('name_merge', 'cat_file')
__cat_output_dir = __input_dir
__cat_input = expand("{dir}/{{sample}}.emapper.seed_orthologs".format(dir=__input_dir), sample=SAMPLES)
__cat_output = "{dir}/{file_name}".format(dir=__cat_output_dir, file_name=__cat_merged_name)
include: __cat_rules
rule all:
input: "{dir}/{file_name}".format(dir=__cat_output_dir, file_name=__cat_merged_name)
snakefiles:
cat: /pasteur/projets/policy01/Atm/snakemake/tools/utils/cat/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:
- test_00000
- test_00001
- test_00002
cat:
name_merge: all.emapper.seed_orthologs
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