diff --git a/pipes/rules/reports.rules b/pipes/rules/reports.rules
index 9d2fc4b33..d4dd4dca3 100644
--- 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
index 0a04d8978..77129e525 100755
--- 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()