Python: Fix generate snakefile

generate_workflow_snakefile.py

@@ -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)"

tools/vcfparser/vcfparser.yaml

@@ -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: