From 569439b66ef9d9d916a08b2d9e52f385e5759eef Mon Sep 17 00:00:00 2001 From: LiaOb21 Date: Thu, 22 Feb 2024 12:41:57 +0000 Subject: [PATCH] making plastid optional --- workflow/rules/oatk.smk | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/workflow/rules/oatk.smk b/workflow/rules/oatk.smk index 74befdc..68dee3d 100644 --- a/workflow/rules/oatk.smk +++ b/workflow/rules/oatk.smk @@ -10,8 +10,12 @@ rule run_oatk: "logs/oatk.log" conda: "../envs/oatk.yaml" + params: + optional_params=" ".join( + f"{k} {v}" for k, v in config["oatk"]["optional_params"].items() if v + ) shell: """ - oatk -k {config[oatk][k]} -c {config[oatk][c]} -t {config[oatk][t]} -m {config[oatk][m]} -p {config[oatk][p]} {input} >> {log} 2>&1 + oatk -k {config[oatk][k]} -c {config[oatk][c]} -t {config[oatk][t]} -m {config[oatk][m]} {params.optional_params} {input} >> {log} 2>&1 mv oatk.asm* results/oatk/ >> {log} 2>&1 """ \ No newline at end of file