fix some report generation and consolidation

broadinstitute · Jan 29, 2015 · 46966d1 · 46966d1
1 parent 7fff3e9
commit 46966d1
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Showing 2 changed files with 2 additions and 1 deletion.
diff --git a/pipes/rules/reports.rules b/pipes/rules/reports.rules
@@ -63,5 +63,5 @@ rule consolidate_spike_count:
                 sample=read_samples_file(config["samples_per_run"]))
     output: '{dir}/summary.spike_count.txt'
     params: logid="all"
-    shell:  "{config[binDir]}/reports.py consolidate_spike_count {dir}/spike_count {output}"
+    shell:  "{config[binDir]}/reports.py consolidate_spike_count {wildcards.dir}/spike_count {output}"
 
diff --git a/reports.py b/reports.py
@@ -203,6 +203,7 @@ def consolidate_spike_count(inDir, outFile):
     '''Consolidate multiple spike count reports into one.'''
     with open(outFile, 'wt') as outf:
         for fn in os.listdir(inDir):
+            fn = os.path.join(inDir, fn)
             s = os.path.basename(fn)
             if not s.endswith('.spike_count.txt'):
                 raise Exception()