Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Metagenomics
snakemake
Commits
e5a53223
Commit
e5a53223
authored
Aug 23, 2021
by
Kenzo-Hugo Hillion
♻
Browse files
fix issues
parent
8eb87e66
Changes
3
Hide whitespace changes
Inline
Side-by-side
tools/cd-hit/Snakefile
View file @
e5a53223
...
...
@@ -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))
tools/cd-hit/example_usage/Snakefile
View file @
e5a53223
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')
...
...
tools/cd-hit/example_usage/config.yaml
View file @
e5a53223
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
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment