Commit e5a53223 authored by Kenzo-Hugo Hillion's avatar Kenzo-Hugo Hillion
Browse files

fix issues

parent 8eb87e66
......@@ -85,22 +85,25 @@ Options
"CD-HIT: accelerated for clustering the next generation sequencing data", Limin Fu, Beifang Niu, Zhengwei Zhu, Sitao Wu & Weizhong Li. Bioinformatics, (2012) 28:3150-3152
"""
__cd-hit_exec_command = config.get('cd-hit', {}).get('exec_command', 'cd-hit')
__cd-hit_modules = config.get('cd-hit', {}).get('modules')
__cd-hit_options = config.get('cd-hit', {}).get('options', '')
__cd_hit_exec_command = config.get('cd_hit', {}).get('exec_command', 'cd_hit')
__cd_hit_modules = config.get('cd_hit', {}).get('modules')
__cd_hit_options = config.get('cd_hit', {}).get('options', '')
__cd_hit_threads = config.get('cd_hit', {}).get('threads', 1)
rule cd-hit:
rule cd_hit:
input:
__cd-hit_input
__cd_hit_input
output:
__cd-hit_output
__cd_hit_output
params:
exec_command = __cd-hit_exec_command,
modules = __cd-hit_modules,
options = __cd-hit_options
exec_command = __cd_hit_exec_command,
modules = __cd_hit_modules,
options = __cd_hit_options
threads:
__cd_hit_threads
run:
command = []
if params.modules:
command.append("module load {params.modules}")
command.append("{params.exec_command} {params.options} -i {input} -o {output}")
command.append("{params.exec_command} {params.options} -i {input} -T {threads} -o {output}")
shell(" && ".join(command))
configfile: "config.yaml"
# ==== Snakefile path ====
__cd-hit_rules = config.get("snakefiles", {}).get("cd-hit")
__cd-hit_rules = config.get("snakefiles", {}).get("cd_hit")
__main_output_dir = config.get('output_dir', 'output')
......
snakefiles:
prodigal: /pasteur/zeus/projets/p02/metasig/gitlab/snakemake/tools/cd-hit/Snakefile
cd_hit: /pasteur/zeus/projets/p02/metasig/gitlab/snakemake/tools/cd-hit/Snakefile
input_dir: /some/input/directory
output_dir: /some/output/directory
......@@ -9,6 +9,7 @@ samples:
- test_00001
- test_00002
prodigal:
cd_hit:
exec_command: cd-hit
modules: blast+/2.10.0 cd-hit
threads: 16
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