From 4b985d2ac95b046e96f0a83cb98f1f5e31fa49bd Mon Sep 17 00:00:00 2001 From: Kevin Murray Date: Mon, 16 Apr 2018 20:31:02 +1000 Subject: [PATCH] Additional fixes to documentation --- docs/CMakeLists.txt | 2 +- docs/algorithm.rst | 2 +- docs/index.rst | 2 +- docs/tutorial.rst | 8 +++----- docs/usage.rst | 1 + 5 files changed, 7 insertions(+), 8 deletions(-) diff --git a/docs/CMakeLists.txt b/docs/CMakeLists.txt index 0a723ce..de292fc 100644 --- a/docs/CMakeLists.txt +++ b/docs/CMakeLists.txt @@ -17,7 +17,7 @@ IF(SPHINXBUILD) COMMAND ${CMAKE_COMMAND} -E remove_directory "${CMAKE_BINARY_DIR}/doc" WORKING_DIRECTORY ${CMAKE_BINARY_DIR} ) - ADD_CUSTOM_TARGET(doc ALL DEPENDS doc_man doc_onehtml) + ADD_CUSTOM_TARGET(doc ALL DEPENDS doc_man doc_html doc_onehtml) INSTALL(FILES ${CMAKE_BINARY_DIR}/doc/man/axe.1 DESTINATION "share/man/man1" RENAME "axe-demux.1") SET_DIRECTORY_PROPERTIES(PROPERTY ADDITIONAL_MAKE_CLEAN_FILES doc/) ELSE() diff --git a/docs/algorithm.rst b/docs/algorithm.rst index 162ba11..1bb1d83 100644 --- a/docs/algorithm.rst +++ b/docs/algorithm.rst @@ -46,7 +46,7 @@ referred to as the 0, 1 and 2-mm tries, for a hamming distance (mismatch) of trie. If this prefix is not a valid leaf in the 0mm trie, we find the longest prefix in the 1mm trie, and so on for all tries in ascending order. If no prefix of the read is a complete sequence in any trie, the read is assigned to -an "non-indexd" output file. +an "non-indexed" output file. This algorithm ensures optimal index matching in many ways, but is also extremely fast. In situations with indexes of differing length, we ensure that diff --git a/docs/index.rst b/docs/index.rst index 6c44c98..5e20398 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -15,7 +15,7 @@ indexing schemes. Contents: .. toctree:: - :maxdepth: 2 + :maxdepth: 1 tutorial usage diff --git a/docs/tutorial.rst b/docs/tutorial.rst index 4329145..233a3f6 100644 --- a/docs/tutorial.rst +++ b/docs/tutorial.rst @@ -2,12 +2,10 @@ Axe Tutorial ************ -**TODO!** - In this tutorial, we'll use Axe to demultiplex some paired-end, combinatorially-index Genotyping-by-Sequencing reads. The data for this -tutorial is available from figshare -`here https://figshare.com/articles/axe-tutorial_tar/6143720`_. +tutorial is available from figshare: +https://figshare.com/articles/axe-tutorial_tar/6143720 . Axe should be run as the initial step of any analysis: don't use sequence QC tools like AdapterRemoval or Trimmomatic before using axe, as indexes may be @@ -54,7 +52,7 @@ Then, we need to ensure that axe has somewhere to put the demultiplexed reads. Axe outputs one file (or more, depending on pairing) per sample. Axe does so by appending the sample name to some prefix (as given by the ``-I``, ``-F``, and/or ``-R`` options). If this prefix is a directory, then sample fastq files -will be created in that subdirectory, but the directory must exist. Let's make +will be created in that sub-directory, but the directory must exist. Let's make an output directory: .. code-block:: bash diff --git a/docs/usage.rst b/docs/usage.rst index fd83eb2..a21eb83 100644 --- a/docs/usage.rst +++ b/docs/usage.rst @@ -18,6 +18,7 @@ For concise reference, the command-line usage of ``axe-demux`` is reproduced below: .. literalinclude:: usage.txt + :language: text Inputs and Outputs ------------------