prevent flu-specific items from being dropped from non-flu tables

Dockerfile

@@ -1,4 +1,4 @@
-ARG MERCURY_VER="1.0.6"
+ARG MERCURY_VER="1.0.7"
 
 FROM google/cloud-sdk:480.0.0-slim
 

README.md

@@ -27,16 +27,16 @@ Default databases by organism:
 We highly recommend using the following Docker image to run Mercury:
 
 ```bash
-docker pull us-docker.pkg.dev/general-theiagen/theiagen/mercury:1.0.6
+docker pull us-docker.pkg.dev/general-theiagen/theiagen/mercury:1.0.7
 ```
 
 The entrypoint for this Docker image is the Mercury help message. To run this container interactively, use the following command:
 
 ```bash
-docker run -it --entrypoint=/bin/bash us-docker.pkg.dev/general-theiagen/theiagen/mercury:1.0.6
+docker run -it --entrypoint=/bin/bash us-docker.pkg.dev/general-theiagen/theiagen/mercury:1.0.7
 # Once inside the container interactively, you can run the tbp-parser tool
 python3 /mercury/mercury/mercury.py -v
-# v1.0.6
+# v1.0.7
 ```
 
 ### Locally with Python

mercury/Table.py

@@ -200,8 +200,9 @@ def make_biosample_csv(self):
       # strip off "Type_" from beginning of Type, e.g. "Type_A" -> "A"
       self.logger.debug("DEBUG:User did not supply isolate or strain metadata columns, creating isolate column for Flu samples now...")
       biosample_metadata["isolate"] = (biosample_metadata["abricate_flu_type"].str.replace("Type_","") + "/" + biosample_metadata["state"] + "/" + biosample_metadata["sample_name"] + "/" + biosample_metadata["year"] + " (" + biosample_metadata["abricate_flu_subtype"] + ")")
-    # Remove 4 extra columns from the output table prior to creating TSV file (these are simply used to create the isolate column)
-    biosample_metadata.drop(["abricate_flu_type", "abricate_flu_subtype", "year", "state"], axis=1, inplace=True)
+
+      # Remove 4 extra columns from the output table prior to creating TSV file (these are simply used to create the isolate column)
+      biosample_metadata.drop(["abricate_flu_type", "abricate_flu_subtype", "year", "state"], axis=1, inplace=True)
 
     biosample_metadata.to_csv(self.output_prefix + "_biosample_metadata.tsv", sep='\t', index=False)
     self.logger.debug("TABLE:BioSample metadata file created")

mercury/__init__.py

@@ -1 +1 @@
-__VERSION__ = "v1.0.6"
+__VERSION__ = "v1.0.7"