From 0d6dd88b58e56de56c6835486cb26c04ffc6f795 Mon Sep 17 00:00:00 2001
From: Robert Bossy <Robert.Bossy@inra.fr>
Date: Tue, 20 Apr 2021 09:04:25 +0200
Subject: [PATCH] added trie serialization step
---
rewrite-taxonomy.snakefile | 12 ++++++++----
1 file changed, 8 insertions(+), 4 deletions(-)
diff --git a/rewrite-taxonomy.snakefile b/rewrite-taxonomy.snakefile
index 9e24389..77b4b3f 100644
--- a/rewrite-taxonomy.snakefile
+++ b/rewrite-taxonomy.snakefile
@@ -5,19 +5,23 @@ rule all:
input:
config['OUTDIR'] + '/finish.txt',
config['OUTDIR'] + '/taxid_microorganisms.txt',
- config['OUTDIR'] + '/taxa+id_microorganisms.txt'
+ config['OUTDIR'] + '/taxa+id_microorganisms.txt',
+ config['OUTDIR'] + '/taxa+id_microorganisms.trie',
+ config['OUTDIR'] + '/taxid_full.txt',
+ config['OUTDIR'] + '/taxa+id_full.txt',
+ config['OUTDIR'] + '/taxa+id_full.trie'
rule check:
input:
- config['OUTDIR'] + '/taxa+id_microorganisms.txt'
+ config['OUTDIR'] + '/taxa+id_{root}.txt'
output:
- config['OUTDIR'] + '/finish.txt'
+ config['OUTDIR'] + '/taxa+id_{root}.trie'
shell:
- '''{config[ALVISNLP]} -J-Xmx12G -alias taxo {input} -alias finish {output} check-taxonomy.plan'''
+ '''{config[ALVISNLP]} -J-Xmx12G -alias taxo {input} -alias trie {output} compile-taxonomy.plan'''
rule microorganisms:
--
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