s/bm_tagger/bmtagger/g

broadinstitute · Nov 13, 2015 · 2f4b8ad · 2f4b8ad
1 parent c7e87c0
commit 2f4b8ad
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Showing 3 changed files with 5 additions and 5 deletions.
diff --git a/docs/pipeuse.rst b/docs/pipeuse.rst
@@ -156,8 +156,8 @@ docs <ftp://ftp.ncbi.nih.gov/pub/agarwala/bmtagger/README.bmtagger.txt>`__.
 
 ::
 
-    "bm_tagger_db_dir":  "/path/to/depletion_databases",
-    "bm_tagger_dbs_remove": [
+    "bmtagger_db_dir":  "/path/to/depletion_databases",
+    "bmtagger_dbs_remove": [
         "hg19",
         "GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA",
         "metagenomics_contaminants_v3"

diff --git a/pipes/config.json b/pipes/config.json
@@ -5,8 +5,8 @@
   "accessions_file_for_lastal_db_build": "",
 
 
-  "bm_tagger_db_dir":  "/idi/sabeti-scratch/kandersen/references/depletion_databases",
-  "bm_tagger_dbs_remove": [
+  "bmtagger_db_dir":  "/idi/sabeti-scratch/kandersen/references/depletion_databases",
+  "bmtagger_dbs_remove": [
     "hg19",
     "GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA",
     "metagenomics_contaminants_v3"],

diff --git a/pipes/rules/hs_deplete.rules b/pipes/rules/hs_deplete.rules
@@ -30,7 +30,7 @@ rule depletion:
     resources: mem=15
     params: LSF=config.get('LSF_queues', {}).get('long', '-q forest'),
             UGER=config.get('UGER_queues', {}).get('long', '-q long'),
-            bmtaggerDbs = expand("{dbdir}/{db}", dbdir=config["bm_tagger_db_dir"], db=config["bm_tagger_dbs_remove"]),
+            bmtaggerDbs = expand("{dbdir}/{db}", dbdir=config["bmtagger_db_dir"], db=config["bmtagger_dbs_remove"]),
             blastDbs = expand("{dbdir}/{db}", dbdir=config["blast_db_dir"], db=config["blast_db_remove"]),
             revert_bam = config["tmp_dir"] +'/'+config["subdirs"]["depletion"]+'/{sample}.raw.bam',
             logid="{sample}"