revise snakemake DBs for BWA

broadinstitute · Feb 23, 2018 · 3a412d2 · 3a412d2
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commit 3a412d2
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Showing 2 changed files with 1 addition and 2 deletions.
diff --git a/pipes/config.yaml b/pipes/config.yaml
@@ -26,8 +26,6 @@ bmtagger_dbs_remove:
 
 bwa_dbs_remove:
   - "s3://sabeti-public-dbs/bmtagger/hg19"
-  - "s3://sabeti-public-dbs/bmtagger/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA"
-  - "s3://sabeti-public-dbs/bmtagger/metagenomics_contaminants_v3"
 
 # Path for the directory containing blast databases used for additional depletion
 # See: ftp://ftp.ncbi.nih.gov/blast/documents/formatdb.html

diff --git a/pipes/rules/hs_deplete.rules b/pipes/rules/hs_deplete.rules
@@ -27,6 +27,7 @@ rule depletion:
         input_bam    = config["data_dir"]+'/'+config["subdirs"]["source"]+'/{sample}.bam',
         bmtagger_dbs = objectify_remote(expand("{db}.{ext}", db=config["bmtagger_dbs_remove"], ext=['bitmask','srprism.ssa','srprism.imp','srprism.idx','srprism.map','srprism.ss','srprism.amp','srprism.rmp','srprism.pmp','srprism.ssd'])),
         blast_dbs    = objectify_remote(expand("{db}.{ext}", db=config["blast_db_remove"], ext=['nhr','nsq','nin'])) # ['nhr','nix','nsq','dict','fai','nin']
+        blast_dbs    = objectify_remote(expand("{db}.{ext}", db=config["bwa_dbs_remove"], ext=['bwt','amb','ann','pac','sa']))
     output: 
         config["tmp_dir"] +'/'+config["subdirs"]["depletion"]+'/{sample}.bwa_depleted.bam',
         config["tmp_dir"] +'/'+config["subdirs"]["depletion"]+'/{sample}.bmtagger_depleted.bam',