update ref_guided_consensus

broadinstitute · Jan 11, 2015 · 49c580d · 49c580d
1 parent f9e51ae
commit 49c580d
Showing 1 changed file with 3 additions and 3 deletions.
diff --git a/pipes/rules/interhost.rules b/pipes/rules/interhost.rules
@@ -28,7 +28,7 @@ rule all_ref_guided:
             config["reportsDir"]+'/summary.coverage_ref.txt.gz'
 
 rule ref_guided_consensus:
-    input:  config["dataDir"]+'/'+config["subdirs"]["source"]+'/{sample}.bam'
+    input:  config["dataDir"]+'/'+config["subdirs"]["depletion"]+'/{sample}.raw.bam'
     output: config["dataDir"]+'/'+config["subdirs"]["align_ref"]+'/{sample}.realigned.bam',
             config["dataDir"]+'/'+config["subdirs"]["align_ref"]+'/{sample}.vcf.gz',
             config["dataDir"]+'/'+config["subdirs"]["align_ref"]+'/{sample}.fasta'
@@ -37,12 +37,12 @@ rule ref_guided_consensus:
             logid="{sample}",
             refGenome=config["ref_genome"],
             novoalign_options="-r Random -l 30 -g 40 -x 20 -t 502",
-            min_coverage="2"
+            min_coverage="3"
     run:
             makedirs(expand("{dir}/{subdir}",
                 dir=[config["dataDir"]],
                 subdir=[config["subdirs"]["align_ref"], config["subdirs"]["assembly"]]))
-            shell("{config[binDir]}/assembly.py refine_assembly {params.refGenome} {input} {output[2]} --outBam {output[0]} --outVcf {output[1]} --min_coverage {params.min_coverage} --novo_params '{params.novoalign_options}' --keep_all_reads")
+            shell("{config[binDir]}/assembly.py refine_assembly {params.refGenome} {input} {output[2]} --outBam {output[0]} --outVcf {output[1]} --min_coverage {params.min_coverage} --novo_params '{params.novoalign_options}' --keep_all_reads --chr_names {wildcards.sample}")
 
 rule ref_guided_diversity:
     input: