From cb1bc65d6c9aad428226414fa0d417e75230fca0 Mon Sep 17 00:00:00 2001 From: Will Rowe Date: Mon, 10 Aug 2020 12:54:39 +0100 Subject: [PATCH] unify underscore hyphen conflicts --- .travis.yml | 2 +- CMakeLists.txt | 2 +- README.md | 24 +++++++++++------------- docs/softmasker.md | 2 +- mkdocs.yml | 16 ++++++++-------- 5 files changed, 22 insertions(+), 24 deletions(-) diff --git a/.travis.yml b/.travis.yml index e3854eb..6093144 100644 --- a/.travis.yml +++ b/.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 diff --git a/CMakeLists.txt b/CMakeLists.txt index ec54221..3883760 100644 --- a/CMakeLists.txt +++ b/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) diff --git a/README.md b/README.md index 0eb0b82..325d4af 100644 --- a/README.md +++ b/README.md @@ -1,11 +1,11 @@

ARTIC tools

-

a bioinformatics pipeline for working with virus sequencing data sequenced with nanopore

+

a set of tools for working with the ARTIC pipeline

- travis + travis Documentation Status - bioconda - License + bioconda + License
--- @@ -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 ``` diff --git a/docs/softmasker.md b/docs/softmasker.md index ff0b43a..bc0947f 100644 --- a/docs/softmasker.md +++ b/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: diff --git a/mkdocs.yml b/mkdocs.yml index e4f1ab0..b6b4d15 100644 --- a/mkdocs.yml +++ b/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"