unify underscore hyphen conflicts

.travis.yml

@@ -53,4 +53,4 @@ script:
   - cmake -DCMAKE_BUILD_TYPE=Debug ..
   - make -j2
   - ../bin/artic_tests
-  - ../bin/artic_tools -v
+  - ../bin/artic-tools -v

CMakeLists.txt

@@ -31,7 +31,7 @@ option(BUILD_TESTING "Build unit tests" ON)
 project(ARTIC)
 
 # set the variables
-set(ARTIC_PROG_NAME artic_tools)
+set(ARTIC_PROG_NAME artic-tools)
 set(ARTIC_VERSION_MAJOR 0)
 set(ARTIC_VERSION_MINOR 1)
 set(ARTIC_VERSION_PATCH 0)

README.md

@@ -1,11 +1,11 @@
 <div align="center">
     <h1>ARTIC tools</h1>
-    <h3>a bioinformatics pipeline for working with virus sequencing data sequenced with nanopore</h3>
+    <h3>a set of tools for working with the ARTIC pipeline</h3>
     <hr>
-    <a href="https://travis-ci.org/will-rowe/artic_tools"><img src="https://travis-ci.org/will-rowe/artic_tools.svg?branch=master" alt="travis"></a>
+    <a href="https://travis-ci.org/will-rowe/artic-tools"><img src="https://travis-ci.org/will-rowe/artic-tools.svg?branch=master" alt="travis"></a>
     <a href='https://artic-tools.readthedocs.io/en/latest/?badge=latest'><img src='https://readthedocs.org/projects/artic-tools/badge/?version=latest' alt='Documentation Status'/></a>
-    <a href="https://bioconda.github.io/recipes/artic_tools/README.html"><img src="https://anaconda.org/bioconda/artic/badges/downloads.svg" alt="bioconda"></a>
-    <a href="https://github.com/will-rowe/artic_tools/blob/master/LICENSE"><img src="https://img.shields.io/badge/license-MIT-orange.svg" alt="License"></a>
+    <a href="https://bioconda.github.io/recipes/artic-tools/README.html"><img src="https://anaconda.org/bioconda/artic-tools/badges/downloads.svg" alt="bioconda"></a>
+    <a href="https://github.com/will-rowe/artic-tools/blob/master/LICENSE"><img src="https://img.shields.io/badge/license-MIT-orange.svg" alt="License"></a>
 </div>
 
 ---
@@ -14,22 +14,20 @@
 
 Work in progress...
 
-This is/will be a set of tools to use in the ARTIC pipeline.
-
-At the moment it can serve as a drop in replacement for the `align_trim` functionality of the pipeline, and can also record a few extra stats and allow some extra alignment filtering.
+At the moment it can serve as a drop in replacement for the `align_trim` functionality of the pipeline, and can also record a few extra stats and allow some extra alignment filtering. See the [docs](https://artic-tools.readthedocs.io/en/latest/softmasker/) for more info on softmasking or checkout the [ARTIC pipeline](https://github.com/artic-network/fieldbioinformatics).
 
 ## Install
 
-`artic_tools` requires CMake and a C++17 compiler.
+`artic-tools` requires CMake and a C++17 compiler.
 
-To download and install `artic_tools` run:
+To download and install `artic-tools` run:
 
 ```
-git clone --recursive https://github.com/will-rowe/artic_tools.git
-mkdir artic_tools/build
-cd artic_tools/build
+git clone --recursive https://github.com/will-rowe/artic-tools.git
+mkdir artic-tools/build
+cd artic-tools/build
 cmake ..
 make -j4
 make test
-../bin/artic_tools -h
+../bin/artic-tools -h
 ```

docs/softmasker.md

@@ -40,7 +40,7 @@ The same inputs and workflow are used, but we have achieved some performance imp
 * during primer search, in the case that a given position is equidistant between two primer sites the upper bound is now used instead of the lower when locating the primer start sites (this typically ends up with more correctly paired primers)
 * output more stats at the end of the report file
 
-The pseudocode for the artic_tools softmasker is:
+The pseudocode for the artic-tools softmasker is:
 
 ```
 for segment in alignment:

mkdocs.yml

@@ -1,11 +1,11 @@
 site_name: artic tools
-repo_url: https://github.com/will-rowe/artic_tools
+repo_url: https://github.com/will-rowe/artic-tools
 theme: readthedocs
 nav:
-  - Home: "index.md"
-  - "User Guide":
-      - "Installation": "installation.md"
-      - "Quick Start": "quick-start.md"
-      - "Commands": "commands.md"
-  - About:
-      - "Softmasker": "softmasker.md"
+    - Home: "index.md"
+    - "User Guide":
+          - "Installation": "installation.md"
+          - "Quick Start": "quick-start.md"
+          - "Commands": "commands.md"
+    - About:
+          - "Softmasker": "softmasker.md"