Merge branch 'master' into 48-join-samples-by-custom-field

bihealth · Apr 23, 2021 · 042ae76 · 042ae76
2 parents a6e5d8e + 7718baa
commit 042ae76
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Showing 15 changed files with 1,436 additions and 161 deletions.
diff --git a/snappy_pipeline/base.py b/snappy_pipeline/base.py
@@ -32,6 +32,10 @@ class UnsupportedActionException(Exception):
     """Raised when user try to call action that isn't supported."""
 
 
+class UnknownFiltrationSourceException(Exception):
+    """Raised when user try to request an unknown filtration source."""
+
+
 def expand_ref(config_path, dict_data, lookup_paths=None, dict_class=OrderedDict):
     """Expand "$ref" in JSON-like data ``dict_data``
 

diff --git a/snappy_pipeline/workflows/abstract/__init__.py b/snappy_pipeline/workflows/abstract/__init__.py
@@ -1006,7 +1006,7 @@ def input_function(wildcards):
                 yield "ped", os.path.realpath(
                     "work/write_pedigree.{index_library}/out/{index_library}.ped"
                 ).format(**wildcards)
-            name_pattern = self.prev_class.name_token.replace(r",[^\.]+", "")
+            name_pattern = self.prev_class.name_pattern.replace(r",[^\.]+", "")
             tpl_path_out = os.path.join("work", name_pattern, "out", name_pattern)
             for key, ext in zip(self.ext_names, self.ext_values):
                 yield key, tpl_path_out.format(ext=ext, **wildcards) + ext