From e5a532235822e5fc54432dda128bd1890878605a Mon Sep 17 00:00:00 2001
From: Kenzo-Hugo Hillion <hillion.kenzo@gmail.com>
Date: Mon, 23 Aug 2021 10:13:18 +0200
Subject: [PATCH] fix issues
---
tools/cd-hit/Snakefile | 23 +++++++++++++----------
tools/cd-hit/example_usage/Snakefile | 2 +-
tools/cd-hit/example_usage/config.yaml | 5 +++--
3 files changed, 17 insertions(+), 13 deletions(-)
diff --git a/tools/cd-hit/Snakefile b/tools/cd-hit/Snakefile
index b91b63d..e023f86 100644
--- a/tools/cd-hit/Snakefile
+++ b/tools/cd-hit/Snakefile
@@ -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))
diff --git a/tools/cd-hit/example_usage/Snakefile b/tools/cd-hit/example_usage/Snakefile
index 0b0cb89..ebd2bfb 100644
--- a/tools/cd-hit/example_usage/Snakefile
+++ b/tools/cd-hit/example_usage/Snakefile
@@ -1,7 +1,7 @@
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')
diff --git a/tools/cd-hit/example_usage/config.yaml b/tools/cd-hit/example_usage/config.yaml
index db42ab7..2bc908f 100644
--- a/tools/cd-hit/example_usage/config.yaml
+++ b/tools/cd-hit/example_usage/config.yaml
@@ -1,5 +1,5 @@
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
--
GitLab