Fix for the lineage_wf command that was causing an invalid marker set…

… to be selected in rare cases when using the reduced_tree flag.

bin/checkm

@@ -642,7 +642,7 @@ i.e. checkm unique will now fail''')
                                             formatter_class=CustomHelpFormatter,
                                             parents=[plot_need_qa_results_parser],
                                             description='Identify outliers in bins relative to reference distributions.',
-                                            epilog='Example: checkm outliers ./bins tetra.tsv outliers.tsv')
+                                            epilog='Example: checkm outliers ./output ./bins tetra.tsv outliers.tsv')
     outlier_parser.add_argument('bin_folder', help="folder containing bins (fasta format)")
     outlier_parser.add_argument('tetra_profile', help='tetranucleotide profiles for each sequence (see tetra command)')
     outlier_parser.add_argument('output_file', help="print results to file")

checkm/DATA_CONFIG

@@ -1 +1 @@
-{"dataRoot": "", "remoteManifestURL": "https://data.ace.uq.edu.au/public/CheckM_databases/", "manifestType": "CheckM", "localManifestName": ".dmanifest", "remoteManifestName": ".dmanifest"}
+{"dataRoot": "", "remoteManifestURL": "https://data.ace.uq.edu.au/public/CheckM_databases/", "manifestType": "CheckM", "remoteManifestName": ".dmanifest", "localManifestName": ".dmanifest"}

checkm/VERSION

@@ -1 +1 @@
-1.0.7
+1.0.8

checkm/markerSets.py

@@ -96,11 +96,23 @@ def setLineageSpecificSelectedMarkerSet(self, selectedMarkerSetMap):
         uid = self.mostSpecificMarkerSet().UID
 
         selectedId = selectedMarkerSetMap[uid]
-
         self.selectedLinageSpecificMarkerSet = None
-        for ms in self.markerSets:
-            if ms.UID == selectedId:
-                self.selectedLinageSpecificMarkerSet = ms
+
+        while not self.selectedLinageSpecificMarkerSet:
+            for ms in self.markerSets:
+                if ms.UID == selectedId:
+                    self.selectedLinageSpecificMarkerSet = ms
+                    break
+
+            if not self.selectedLinageSpecificMarkerSet:
+                # This is a hack for the reduced tree. Since not all
+                # marker sets are in the reduced tree it is possible the
+                # selected marker set might not be avaliable. In this case,
+                # we should move to the next suitable marker set. Ideally,
+                # this could be avoided by just forcing in the selected
+                # marker set.
+                selectedId = selectedMarkerSetMap[selectedId]
+            else:
                 break
 
         if self.selectedLinageSpecificMarkerSet == None: