diff --git a/rewrite-taxonomy.snakefile b/rewrite-taxonomy.snakefile index 40c22f63b8e7c5660ef2de71010e6422052ed323..9e24389f7bf8d274bfc6521ed6f419346d4862ad 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: