From 89d6131038c2f158df7fb640a8e3c667d676039a Mon Sep 17 00:00:00 2001
From: Robert Bossy <Robert.Bossy@inra.fr>
Date: Mon, 5 Apr 2021 16:42:56 +0200
Subject: [PATCH] snakefiles bug fixes
---
config.yaml | 2 +-
dsmz-download.snakefile | 2 +-
dsmz-match.snakefile | 5 ++---
rewrite-taxonomy.snakefile | 2 +-
4 files changed, 5 insertions(+), 6 deletions(-)
diff --git a/config.yaml b/config.yaml
index ffa7e07..ad0dadc 100644
--- a/config.yaml
+++ b/config.yaml
@@ -9,7 +9,7 @@ REWRITE_TAXONOMY: '~/code/bibliome-java-utils/test/install/bin/rewrite-taxonomy'
# Output and working directories
-OUTDIR: 'test'
+OUTDIR: 'output'
diff --git a/dsmz-download.snakefile b/dsmz-download.snakefile
index 6ac2e99..e37a515 100644
--- a/dsmz-download.snakefile
+++ b/dsmz-download.snakefile
@@ -6,4 +6,4 @@ rule download:
output:
directory(config['OUTDIR'] + '/' + config['DSMZ_STRAINS_DIR'])
- shell: '''./bacdive.py -o {output} -u {config[BACDIVE_USER]} -P {config[BACDIVE_PASSWORD_FILE]} -x -a __dummy'''
+ shell: '''bacdive.py -o {output} -u {config[BACDIVE_USER]} -P {config[BACDIVE_PASSWORD_FILE]} -x -a __dummy'''
diff --git a/dsmz-match.snakefile b/dsmz-match.snakefile
index 672a553..046df2b 100644
--- a/dsmz-match.snakefile
+++ b/dsmz-match.snakefile
@@ -10,7 +10,6 @@ rule match:
directory(config['OUTDIR'] + '/' + config['DSMZ_MATCH_DIR'])
input:
- match='./dsmz-match.py',
- strains=config['OUTDIR'] + '/' + config['DSMZ_STRAINS_DIR']
+ config['OUTDIR'] + '/' + config['DSMZ_STRAINS_DIR']
- shell: '''{input.match} {config[NCBI_DIR]}/nodes.dmp {config[NCBI_DIR]}/names.dmp {input.strains} {output}'''
+ shell: '''./dsmz-match.py {config[OUTDIR]}/{config[NCBI_DIR]}/nodes.dmp {config[OUTDIR]}/{config[NCBI_DIR]}/names.dmp {input} {output}'''
diff --git a/rewrite-taxonomy.snakefile b/rewrite-taxonomy.snakefile
index 9acf158..c7a2e2a 100644
--- a/rewrite-taxonomy.snakefile
+++ b/rewrite-taxonomy.snakefile
@@ -20,4 +20,4 @@ rule full:
config['OUTDIR'] + '/' + config['DSMZ_MATCH_DIR']
shell:
- '''{config[REWRITE_TAXONOMY]} -namesFile {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[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}'''
--
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