snakefiles bug fixes

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'
 
 
 

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'''

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}'''

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}'''