Bumping up minor version for new feature

OpenOmics · Jun 5, 2024 · c20b602 · c20b602
1 parent 85b5f74
commit c20b602
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diff --git a/VERSION b/VERSION
@@ -1 +1 @@
-0.1.0
+0.2.0
diff --git a/docker/mpox-seek/README.md b/docker/mpox-seek/README.md
@@ -8,20 +8,20 @@ docker image ls
 
 # Build from Dockerfile
 ln -f ../../workflow/envs/mpox.yaml .
-docker build --no-cache -f Dockerfile --tag=mpox-seek:v0.1.0 .
+docker build --no-cache -f Dockerfile --tag=mpox-seek:v0.2.0 .
 
 # Testing, take a peek inside
-docker run -ti mpox-seek:v0.1.0 /bin/bash
+docker run -ti mpox-seek:v0.2.0 /bin/bash
 
 # Updating Tag  before pushing to DockerHub
-docker tag mpox-seek:v0.1.0 skchronicles/mpox-seek:v0.1.0
-docker tag mpox-seek:v0.1.0 skchronicles/mpox-seek         # latest
+docker tag mpox-seek:v0.2.0 skchronicles/mpox-seek:v0.2.0
+docker tag mpox-seek:v0.2.0 skchronicles/mpox-seek         # latest
 
 # Check out new tag(s)
 docker image ls
 
 # Push new tagged image to DockerHub
-docker push skchronicles/mpox-seek:v0.1.0
+docker push skchronicles/mpox-seek:v0.2.0
 docker push skchronicles/mpox-seek:latest
 ```
 
@@ -30,7 +30,7 @@ docker push skchronicles/mpox-seek:latest
 Scan your image for known vulnerabilities:
 
 ```bash
-docker scan mpox-seek:v0.1.0
+docker scan mpox-seek:v0.2.0
 ```
 
 > **Please Note**: Any references to `skchronicles` should be replaced your username if you would also like to push the image to a non-org account.
diff --git a/docs/usage/run.md b/docs/usage/run.md
@@ -82,6 +82,16 @@ Each of the following arguments are optional, and do not need to be provided.
 > 
 > ***Example:*** `--bootstrap-trees`
 
+---
+  `--plot-coverage`  
+> **Plots coverage of each sample.**  
+> *type: boolean flag*  
+> *default: false*  
+>  
+>  This option will plot coverage along the reference genome. If this flag is provided, per-sample plots of raw coverage will be created. This plot can be useful for identifying samples or regions of the reference genome with low coverage. By default, the pipeline will not create any coverage plots.  
+>  
+> ***Example:*** `--plot-coverage`  
+
 ### 2.3 Orchestration options
 
 Each of the following arguments are optional, and do not need to be provided. 

diff --git a/mpox-seek b/mpox-seek
@@ -473,11 +473,9 @@ def parsed_arguments(name, description):
         
           --plot-coverage
                                 Plots coverage of along the reference genome. If this flag            
-                                is provided, per-sample plots of raw and library normalized 
-                                coverage will be created. This plot can be useful for ident-
-                                ifying samples or regions of the reference genome with low 
-                                coverage. The library normalized coverage track is useful 
-                                for comparing coverage across samples.
+                                is provided, per-sample plots of raw coverage will be made. 
+                                This plot can be useful for identifying samples or regions
+                                of the reference genome with low coverage. 
                                   Example: --plot-coverage
 
         {3}{4}Orchestration options:{5}