From 6296afce835c6022f4016c09af6f76dda5fb9a91 Mon Sep 17 00:00:00 2001
From: nikos <n.pappas@uu.nl>
Date: Tue, 12 Jan 2021 17:41:37 +0100
Subject: [PATCH] update workflow for lca rule
---
workflow/Snakefile | 12 ++++++++++++
1 file changed, 12 insertions(+)
diff --git a/workflow/Snakefile b/workflow/Snakefile
index 7839343..0b77579 100644
--- a/workflow/Snakefile
+++ b/workflow/Snakefile
@@ -54,6 +54,7 @@ rule all:
"results/{sample}/tmp/reflist.txt",
"results/{sample}/{tool}/predictions.tsv",
"results/{sample}/all_predictions.tsv",
+ "results/{sample}/lca.tsv"
],
sample=SAMPLES, tool= TOOLS)
@@ -282,3 +283,14 @@ rule collect_hosts:
"<(cut -f2,3 {input[3]}) "
">>{output.sample_tsv}"
+rule lca:
+ input:
+ predictions_tsv = rules.collect_hosts.output.sample_tsv
+ output:
+ lca_tsv = "results/{sample}/lca.tsv"
+ log:
+ "logs/{sample}/lca.log"
+ shell:
+ "python workflow/scripts/get_lca.py "
+ "-i {input.predictions_tsv} "
+ "-o {output.lca_tsv} &>{log}"
--
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