diff --git a/snappy_pipeline/workflows/hla_typing/Snakefile b/snappy_pipeline/workflows/hla_typing/Snakefile index 5b07da66..3dc829c5 100644 --- a/snappy_pipeline/workflows/hla_typing/Snakefile +++ b/snappy_pipeline/workflows/hla_typing/Snakefile @@ -53,6 +53,7 @@ rule hla_typing_link_in_run: # Generic linking out --------------------------------------------------------- + rule hla_typing_link_out_run: input: wf.get_input_files("link_out", "run"), @@ -67,6 +68,7 @@ rule hla_typing_link_out_run: # OptiType -------------------------------------------------------------------- if "optitype" in wf.w_config.step_config["hla_typing"].tools: + rule hla_typing_optitype_run: input: **wf.get_input_files("optitype", "run"), @@ -91,6 +93,7 @@ if "optitype" in wf.w_config.step_config["hla_typing"].tools: # NB: reference is updated in the installed package if "arcashla" in wf.w_config.step_config["hla_typing"].tools: + rule hla_typing_arcashla_prepare_reference: output: touch("work/arcashla.prepare_reference/out/.done"), @@ -99,7 +102,6 @@ if "arcashla" in wf.w_config.step_config["hla_typing"].tools: wrapper: wf.wrapper_path("arcashla/prepare_reference") - rule hla_typing_arcashla_run: input: unpack(wf.get_input_files("arcashla", "run")),