Source decorator to apply wildcards to outputs.

This is used to circumvent the change in behaviour in snakemake.
https://bitbucket.org/snakemake/snakemake/issues/956/placeholders-not-properly-matched-with

libworkflows/libworkflows/__init__.py

@@ -7,4 +7,4 @@ from .libworkflows import (
     sum_feature_counts, sum_htseq_counts, sum_intersect_counts,
     test_na_file,
     texscape,
-    warn_context)
+    warn_context, wc_applied)

libworkflows/libworkflows/libworkflows.py

@@ -10,6 +10,7 @@ import matplotlib as mpl
 import matplotlib.pyplot as plt
 from re import compile, sub
 from snakemake import shell
+from snakemake.io import apply_wildcards
 # To parse genome size information
 from bs4 import BeautifulSoup
 
@@ -108,6 +109,25 @@ def ensure_relative(path, basedir):
     else:
         return path
 
+
+def wc_applied(source_function):
+    """
+    This can be used as a decorator for rule input sourcing functions.
+
+    This ensures that results returned in the form of explicit output from a
+    rule has the wildcard substitution applied.
+
+    See <https://bitbucket.org/snakemake/snakemake/issues/956/placeholders-not-properly-matched-with>.
+    """
+    def wc_applied_source_func(wildcards):
+        filename_templates = source_function(wildcards)
+        if not isinstance(filename_templates, (str, bytes)):
+            return [apply_wildcards(filename_template, wildcards) for filename_template in filename_templates]
+        else:
+            return apply_wildcards(filename_templates, wildcards)
+    return wc_applied_source_func
+
+
 def cleanup_and_backup(output_dir, config):
     """Performs cleanup and backup according to the information present in the
     *config* dictionary."""