Ensure passed in sample names get treated as strings when parsed from…

… YAML as integers #25
chapmanb · Jan 15, 2015 · 70d0a07 · 70d0a07
1 parent 58dfd75
commit 70d0a07
Showing 1 changed file with 3 additions and 0 deletions.
diff --git a/src/bcbio/variation/config.clj b/src/bcbio/variation/config.clj
@@ -161,12 +161,15 @@
                  (string? val) (make-absolute val)
                  :else val)
                 val))
+            (sample? [path k]
+              (or (= k :sample) (= (last path) :sample)))
             (update-tree [config path]
               (cond (map? config)
                     (reduce (fn [item [k v]]
                               (assoc item k (cond
                                              (map? v) (update-tree v (conj path k))
                                              (seq? v) (map #(update-tree % (conj path k)) v)
+                                             (sample? path k) (str v)
                                              :else (maybe-process v (conj path k)))))
                             config
                             (vec config))