Merge branch 'master' into ct-refactor-easy-deploy-broad

broadinstitute · Jul 1, 2016 · 0cf838d · 0cf838d
2 parents c5ed88e + b057c17
commit 0cf838d
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Showing 3 changed files with 5 additions and 2 deletions.
diff --git a/pipes/rules/hs_deplete.rules b/pipes/rules/hs_deplete.rules
@@ -65,7 +65,10 @@ rule filter_to_taxon:
 
 def merge_one_per_sample_inputs(wildcards):
     if 'seqruns_demux' not in config or not os.path.isfile(config['seqruns_demux']):
-        return config["data_dir"]+'/'+config["subdirs"]["depletion"] +'/'+ wildcards.sample + '.' + wildcards.adjective + '.bam'
+        if wildcards.adjective == 'raw':
+            return config["data_dir"] + '/' + config["subdirs"]["source"] + '/' + wildcards.sample + '.bam'
+        else:
+            return config["data_dir"]+'/'+config["subdirs"]["depletion"] +'/'+ wildcards.sample + '.' + wildcards.adjective + '.bam'
     runs = set()
     for lane in read_tab_file(config['seqruns_demux']):
         for well in read_tab_file(lane['barcode_file']):

diff --git a/requirements-tests.txt b/requirements-tests.txt
@@ -1,3 +1,4 @@
+pytest==2.9.1
 coveralls==1.1
 pycodestyle
 mock==2.0.0

diff --git a/requirements.txt b/requirements.txt
@@ -4,6 +4,5 @@
 biopython==1.64
 future>=0.15.2
 futures==3.0.3; python_version == '2.6' or python_version=='2.7'
-pytest==2.9.1
 pysam==0.8.3
 PyYAML==3.11