From 12bc018fa0db5bfcb311ce2ae842457a46c5d7c2 Mon Sep 17 00:00:00 2001
From: Robert Bossy <Robert.Bossy@inra.fr>
Date: Fri, 16 Apr 2021 10:11:09 +0200
Subject: [PATCH] fixed rewrite snakefile top goal
---
rewrite-taxonomy.snakefile | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)
diff --git a/rewrite-taxonomy.snakefile b/rewrite-taxonomy.snakefile
index 40c22f6..9e24389 100644
--- a/rewrite-taxonomy.snakefile
+++ b/rewrite-taxonomy.snakefile
@@ -4,7 +4,8 @@ configfile: 'config.yaml'
rule all:
input:
config['OUTDIR'] + '/finish.txt',
- config['OUTDIR'] + '/taxid_microorganisms.txt'
+ config['OUTDIR'] + '/taxid_microorganisms.txt',
+ config['OUTDIR'] + '/taxa+id_microorganisms.txt'
rule check:
@@ -39,7 +40,7 @@ rule taxaid_full:
config['OUTDIR'] + '/' + config['DSMZ_MATCH_DIR']
shell:
- '''{config[REWRITE_TAXONOMY]} -namesFile {config[OUTDIR]}/{config[NCBI_DIR]}/names.dmp -namesFile {input}/dsmz-names.dmp -prefix ncbi: -rejectionFile reject.txt -saturationFile saturate.txt -pattern '{{NAME}}\t{{TAXID}}\t{{CANONICAL}}\t{{TAXID_PATH}}\t{{POS_TAG}}\t{{RANK}}\t{{SPECIES_TAXID}}\t{{SPECIES_NAME}}\n' {config[OUTDIR]}/{config[NCBI_DIR]}/nodes.dmp {input}/dsmz-nodes.dmp >{output}'''
+ '''{config[REWRITE_TAXONOMY]} -namesFile {config[OUTDIR]}/{config[NCBI_DIR]}/names.dmp -namesFile {input}/dsmz-names.dmp -prefix ncbi: -rejectionFile reject.txt -saturationFile saturate.txt -pattern '{{NAME}}\t{{TAXID}}\t{{CANONICAL}}\t{{TAXID_PATH}}\t{{POS_TAG}}\t{{RANK}}\t{{SPECIES_TAXID}}\t{{SPECIES_NAME}}\n' {config[OUTDIR]}/{config[NCBI_DIR]}/nodes.dmp {input}/dsmz-nodes.dmp >{output}'''
rule taxid_full:
--
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