From 6af6b32854018803e4b9c9c062de1df61ab3bfa7 Mon Sep 17 00:00:00 2001 From: Kenzo-Hugo Hillion <hillion.kenzo@gmail.com> Date: Tue, 17 Aug 2021 09:56:05 +0200 Subject: [PATCH] fix rules --- tools/prodigal/Snakefile | 9 ++++----- tools/prodigal/example_usage/Snakefile | 2 +- 2 files changed, 5 insertions(+), 6 deletions(-) diff --git a/tools/prodigal/Snakefile b/tools/prodigal/Snakefile index b9da109..b304ade 100644 --- a/tools/prodigal/Snakefile +++ b/tools/prodigal/Snakefile @@ -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 = [] diff --git a/tools/prodigal/example_usage/Snakefile b/tools/prodigal/example_usage/Snakefile index 7861e92..4b32331 100644 --- a/tools/prodigal/example_usage/Snakefile +++ b/tools/prodigal/example_usage/Snakefile @@ -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) -- GitLab