Merge pull request #11 from nf-core/dev

Doc update before release
nf-core · Apr 29, 2019 · e69aa3d · e69aa3d
2 parents 47cc6f4 + 6f5b46e
commit e69aa3d
Show file tree

Hide file tree

Showing 21 changed files with 156 additions and 360 deletions.
diff --git a/.gitignore b/.gitignore
@@ -7,3 +7,6 @@ tests/test_data
 *.ipynb_checkpoints
 docs/build/
 test/
+_build
+_static
+_templates
diff --git a/README.md b/README.md
@@ -2,25 +2,26 @@
 [![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A50.32.0-brightgreen.svg)](https://www.nextflow.io/)
 [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg)](http://bioconda.github.io/)
 [![Docker](https://img.shields.io/docker/automated/nfcore/coproid.svg)](https://hub.docker.com/r/nfcore/coproid)
+[![Documentation Status](https://readthedocs.org/projects/coproid/badge/?version=latest)](https://coproid.readthedocs.io/en/latest/?badge=latest)
 
-# ![logo_coproid](docs/source/_static/img/coproid_logo_small.jpg) ![logo_nf_core](assets/img/coproID_nf-core_logo_small.png) 
+# ![logo_coproid](assets/img/coproid_logo_small.jpg) ![logo_nf_core](assets/img/coproID_nf-core_logo_small.png)
 
 ## Documentation
 
 The nf-core/coproid pipeline comes with documentation about the pipeline, found in the `docs/` directory:
 
-1. [Installation](https://nf-co.re/usage/installation)
-2. Pipeline configuration
-    * [Local installation](https://nf-co.re/usage/local_installation)
-    * [Adding your own system config](https://nf-co.re/usage/adding_own_config)
-    * [Reference genomes](https://nf-co.re/usage/reference_genomes)
-3. [Running the pipeline](docs/usage.md)
-4. [Output and how to interpret the results](docs/output.md)
-5. [Troubleshooting](https://nf-co.re/usage/troubleshooting)
+1.  [Installation](https://nf-co.re/usage/installation)
+2.  Pipeline configuration
+    -   [Local installation](https://nf-co.re/usage/local_installation)
+    -   [Adding your own system config](https://nf-co.re/usage/adding_own_config)
+    -   [Reference genomes](https://nf-co.re/usage/reference_genomes)
+3.  [Running the pipeline](docs/usage.md)
+4.  [Output and how to interpret the results](docs/output.md)
+5.  [Troubleshooting](https://nf-co.re/usage/troubleshooting)
 
 ## Introduction
 
-**CoproID** helps you to identify the *"true maker"* of a sequenced Coprolite by checking the microbiome composition and the endogenous DNA.
+**CoproID** helps you to identify the _"true maker"_ of a sequenced Coprolite by checking the microbiome composition and the endogenous DNA.
 
 The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible.
 

diff --git a/assets/img/coproid_dag.png b/assets/img/coproid_dag.png
diff --git a/...source/_static/img/coproid_logo_small.jpg → assets/img/coproid_logo_small.jpg b/...source/_static/img/coproid_logo_small.jpg → assets/img/coproid_logo_small.jpg
diff --git a/assets/multiqc_config.yaml b/assets/multiqc_config.yaml
@@ -1,5 +1,5 @@
-title: "Metrics Results of coproID"
-intro_text: "This reports summarises analysis results generated by coproID"
+title: "Results of coproID"
+intro_text: "This reports summarizes results generated by coproID"
 
 report_comment: >
     This report has been generated by the <a href="https://github.com/nf-core/coproid" target="_blank">nf-core/coproid</a>
@@ -8,6 +8,10 @@ report_comment: >
 
 export_plots: true
 
+custom_logo: 'coproid_logo_small.jpg'
+custom_logo_url: 'https://github.com/nf-core/coproid'
+custom_logo_title: 'github.com/nf-core/coproid'
+
 report_section_order:
     nf-core/coproid-software-versions:
         order: -1000

diff --git a/bin/scrape_software_versions.py b/bin/scrape_software_versions.py
@@ -3,7 +3,6 @@
 from collections import OrderedDict
 import re
 
-# TODO nf-core: Add additional regexes for new tools in process get_software_versions
 regexes = {
     'nf-core/coproid': ['v_pipeline.txt', r"(\S+)"],
     'Nextflow': ['v_nextflow.txt', r"(\S+)"],
@@ -14,7 +13,8 @@
     'Kraken2': ['v_kraken2.txt', r"Kraken\sversion\s(\S+)"],
     'MultiQC': ['v_multiqc.txt', r"multiqc, version (\S+)"],
     'Sourcepredict': ['v_sourcepredict.txt', r"SourcePredict\sv(\d*\.\d*)"],
-    'Samtools': ['v_samtools.txt', r"samtools\s(\S+)"]
+    'Samtools': ['v_samtools.txt', r"samtools\s(\S+)"],
+    'Python': ['v_python.txt', r'Python\s(\S+)']
 }
 results = OrderedDict()
 results['nf-core/coproid'] = '<span style="color:#999999;\">N/A</span>'

diff --git a/docs/Makefile b/docs/Makefile
@@ -4,9 +4,9 @@
 # You can set these variables from the command line.
 SPHINXOPTS    =
 SPHINXBUILD   = sphinx-build
-SPHINXPROJ    = coproid
-SOURCEDIR     = source
-BUILDDIR      = build
+SPHINXPROJ    = coproID
+SOURCEDIR     = .
+BUILDDIR      = _build
 
 # Put it first so that "make" without argument is like "make help".
 help:

diff --git a/docs/source/conf.py → docs/conf.py b/docs/source/conf.py → docs/conf.py
@@ -22,16 +22,17 @@
     '.md': CommonMarkParser,
 }
 
+
 # -- Project information -----------------------------------------------------
 
-project = 'coproid'
+project = 'nf-core/coproID'
 copyright = '2019, Maxime Borry'
 author = 'Maxime Borry'
 
 # The short X.Y version
 version = ''
 # The full version, including alpha/beta/rc tags
-release = ''
+release = '1.0'
 
 
 # -- General configuration ---------------------------------------------------
@@ -48,9 +49,7 @@
     'sphinx.ext.doctest',
     'sphinx.ext.intersphinx',
     'sphinx.ext.todo',
-    'sphinx.ext.coverage',
     'sphinx.ext.mathjax',
-    'sphinx.ext.ifconfig',
     'sphinx.ext.viewcode',
     'sphinx.ext.githubpages',
 ]
@@ -61,8 +60,8 @@
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
 #
-# source_suffix = ['.rst', '.md']
 source_suffix = ['.rst', '.md']
+# source_suffix = '.rst'
 
 # The master toctree document.
 master_doc = 'index'
@@ -77,7 +76,7 @@
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path .
-exclude_patterns = []
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
 
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = 'sphinx'
@@ -88,6 +87,7 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
+# html_theme = 'alabaster'
 html_theme = 'sphinx_rtd_theme'
 
 # Theme options are theme-specific and customize the look and feel of a theme
@@ -115,7 +115,7 @@
 # -- Options for HTMLHelp output ---------------------------------------------
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'coproiddoc'
+htmlhelp_basename = 'coproIDdoc'
 
 
 # -- Options for LaTeX output ------------------------------------------------
@@ -142,7 +142,7 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'coproid.tex', 'coproid Documentation',
+    (master_doc, 'coproID.tex', 'coproID Documentation',
      'Maxime Borry', 'manual'),
 ]
 
@@ -152,7 +152,7 @@
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    (master_doc, 'coproid', 'coproid Documentation',
+    (master_doc, 'coproid', 'coproID Documentation',
      [author], 1)
 ]
 
@@ -163,8 +163,8 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'coproid', 'coproid Documentation',
-     author, 'coproid', 'One line description of project.',
+    (master_doc, 'coproID', 'coproID Documentation',
+     author, 'coproID', 'One line description of project.',
      'Miscellaneous'),
 ]
 
@@ -201,3 +201,13 @@
 
 # If true, `todo` and `todoList` produce output, else they produce nothing.
 todo_include_todos = True
+
+# doc_root = "file:///Users/borry/Documents/GitHub/coproID/docs/_build/html/"
+
+
+# def setup(app):
+#     app.add_config_value('recommonmark_config', {
+#         'url_resolver': lambda url: doc_root + url,
+#         'auto_toc_tree_section': 'Contents',
+#     }, True)
+#     app.add_transform(AutoStructify)
diff --git a/docs/configuration.md b/docs/configuration.md
@@ -0,0 +1,10 @@
+# Configuration
+
+This part of the documentation (common to all nf-core pipelines) is hosted on [nf-co.re
+](https://nf-co.re/)
+
+## Pipeline configuration
+
+-   [Local installation](https://nf-co.re/usage/local_installation)
+-   [Adding your own system config](https://nf-co.re/usage/adding_own_config)
+-   [Reference genomes](https://nf-co.re/usage/reference_genomes)
diff --git a/docs/source/index.rst → docs/index.rst b/docs/source/index.rst → docs/index.rst
@@ -1,21 +1,21 @@
-.. coproid documentation master file, created by
-   sphinx-quickstart on Tue Apr 23 18:30:28 2019.
+.. coproID documentation master file, created by
+   sphinx-quickstart on Mon Apr 29 14:50:51 2019.
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
-Welcome to coproid's documentation!
+Welcome to coproID's documentation!
 ===================================
 
 .. toctree::
    :maxdepth: 2
    :caption: Contents:
 
-   intro
+   introduction
    installation
+   configuration
    usage
-   methods
    output
-   troubleshooting
+
 
 
 Indices and tables

diff --git a/docs/installation.md b/docs/installation.md
@@ -0,0 +1,6 @@
+# Installation
+
+This part of the documentation (common to all nf-core pipelines) is hosted on [nf-co.re
+](https://nf-co.re/)
+
+[nf-co.re/usage/installation](https://nf-co.re/usage/installation)
diff --git a/docs/introduction.md b/docs/introduction.md
@@ -0,0 +1,27 @@
+# Introduction
+
+![logo](../assets/img/coproid_logo_small.jpg) ![nf-core-logo](../assets/img/coproID_nf-core_logo_small.png)
+
+**coproID** (**CO**prolite **ID**entification) is a tool developed at the
+[Max Planck insitute for the Science of Human History](http://www.shh.mpg.de/en)
+by [Maxime Borry](https://github.com/maxibor)
+
+The purpose of **coproID** is to help identify the host of given sequence microbiome when there is a doubt between species.
+
+**coproID** is a pipeline developed using [Nextflow](https://www.nextflow.io/) and made available through [nf-core](https://github.com/nf-core)
+
+Even though it was developed with coprolite host identification in mind, it can be applied to any microbiome, provided they contain host DNA.
+
+## Quick start
+
+Example:
+
+    nextflow run maxibor/coproid --genome1 'GRCh37' --genome2 'CanFam3.1' --name1 'Homo_sapiens' --name2 'Canis_familiaris' --reads '*_R{1,2}.fastq.gz'
+
+## coproID example workFlow
+
+![dag](../assets/img/coproid_dag.png)
+
+## How to cite coproID
+
+The coproID article is coming.
diff --git a/docs/source/_static/img/coproid_dag.png b/docs/source/_static/img/coproid_dag.png
diff --git a/docs/source/installation.md b/docs/source/installation.md
diff --git a/docs/source/intro.md b/docs/source/intro.md