Commit 3a82de07 authored by root's avatar root
Browse files

Python: Fix generate snakefile

parent 8d7302a4
......@@ -98,8 +98,12 @@ def generate(name, path_yaml = "", path_input = DEFAULT_PATH_INPUT, path_output
for command in tool_yaml["commands"]:
if command["name"] == step["rule_name"]:
for output in command["outputs"]:
if "{sample}" in output["file"]:
need_expand = True
if "file" in output:
if "{sample}" in output["file"]:
need_expand = True
else:
# TODO return error
continue
if need_expand:
expand_start = "expand("
expand_end = ", sample=SAMPLES)"
......
......@@ -18,7 +18,7 @@
output_dir: vcfparser,
inputs: [{ name: vcfs, type: "vcf" }],
outputs: [
{name: vcf_plots_mqc, type: "tsv"}
{name: vcf_plots_mqc, type: "tsv", file: "vcf_plots_mqc_list.tsv"}
#{ name: "List of plots files", file: "vcf_plots_mqc_list.tsv", description: "List of plots files generated and included in the final report" }
],
options:
......
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