Commit 6af6b328 authored by Kenzo-Hugo Hillion's avatar Kenzo-Hugo Hillion
Browse files

fix rules

parent d8eb2eec
......@@ -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 = []
......
......@@ -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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