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Metagenomics
snakemake
Commits
6af6b328
Commit
6af6b328
authored
Aug 17, 2021
by
Kenzo-Hugo Hillion
♻
Browse files
fix rules
parent
d8eb2eec
Changes
2
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tools/prodigal/Snakefile
View file @
6af6b328
...
...
@@ -23,20 +23,19 @@ Usage: prodigal [-a trans_file] [-c] [-d nuc_file] [-f output_type]
-v: Print version number and exit.
"""
__prodigal_exec_command = config.get(
'prodigal', {}
).get('exec_command', 'prodigal')
__prodigal_exec_command = config.get('prodigal', {}).get('exec_command', 'prodigal')
__prodigal_modules = config.get('prodigal', {}).get('modules')
__prodigal_options = config.get('prodigal', {}).get('options', '')
rule prodigal:
input:
__prodigal_input
output:
fasta_genes = __prodigal_fasta_genes
fasta_genes = __prodigal_fasta_genes
,
genes = __prodigal_genes
params:
exec_command = __prodigal_exec_command,
modules = __prodigal_modules
modules = __prodigal_modules
,
options = __prodigal_options
run:
command = []
...
...
tools/prodigal/example_usage/Snakefile
View file @
6af6b328
...
...
@@ -18,5 +18,5 @@ include: __prodigal_rules
rule all:
input:
fasta_genes = expand("{dir}/{{sample}}.fa".format(dir=__prodigal_output_dir), sample=SAMPLES)
fasta_genes = expand("{dir}/{{sample}}.fa".format(dir=__prodigal_output_dir), sample=SAMPLES)
,
genes = expand("{dir}/{{sample}}.gbk".format(dir=__prodigal_output_dir), sample=SAMPLES)
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