nextstrain · eharkins · Nov 20, 2020
diff --git a/docs/contribute/DEV_DOCS.md b/docs/contribute/DEV_DOCS.md
@@ -1,4 +1,14 @@
 # Augur Development Docs for Contributors
+<!-- WARNING -->
+<!-- Do not edit this file from within the docs.nextstrain.org repository. -->
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+<!-- WARNING -->
+<!-- WARNING -->
+<!-- WARNING -->
 
 Thank you for helping us to improve Augur! This document describes:
 

diff --git a/docs/examples/examples.rst b/docs/examples/examples.rst
@@ -1,6 +1,17 @@
 =============================
 Examples of Augur in the wild
 =============================
+..
+   WARNING
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+   WARNING
+   WARNING
+   WARNING
 
 We really enjoy hearing about people using Augur.  If you use Augur to do your
 work, we'd love to add it to this page!  Let us know about it by `opening an

diff --git a/docs/faq/colors.md b/docs/faq/colors.md
@@ -1,4 +1,14 @@
 # Adding Custom Trait Colors
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+<!-- WARNING -->
+<!-- WARNING -->
+<!-- WARNING -->
 
 Auspice uses a number of default color schemes to color the tree using meta data or values that the augur pipeline computed. In some cases these defaults are not suitable for particular type of data, and you'd like to use your own color schemes.
 

diff --git a/docs/faq/fasta_input.md b/docs/faq/fasta_input.md
@@ -1,4 +1,14 @@
 # Using Fasta Input
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+<!-- WARNING -->
 
 If you would like to run augur on viral data, or bacterial SNP data, you probably would like to start with Fasta sequence data.
 
@@ -8,4 +18,4 @@ Your sequence data should
 
 * consist of homologous sequences that can be aligned unambiguously
 * needs to contain sufficient diversity to allow reliable tree reconstruction
-* should be of similar length. Mixing short sequences (300bp) with much longer ones (10000bp) often yields unexpected results.
+* should be of similar length. Mixing short sequences (300bp) with much longer ones (10000bp) often yields unexpected results.
diff --git a/docs/faq/import-beast.md b/docs/faq/import-beast.md
@@ -1,4 +1,15 @@
 ## Importing BEAST MCC trees into augur
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+
 
 This documentation details how to import BEAST MCC trees using `augur import beast`.
 Currently this is most useful for producing auspice-compatable output using `augur export`, however in the future we will provide instructions on how to perform additional analysis using other augur tools.

diff --git a/docs/faq/lat_longs.md b/docs/faq/lat_longs.md
@@ -1,4 +1,14 @@
 # Adding Custom Lat-Long Data
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+<!-- WARNING -->
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+<!-- WARNING -->
 
 To place sequences on a map, auspice needs to know where the locations you specify are on the globe. These coordinates are provided by augur and augur has preset coordinates for many places. For example, for `region`, `country`, and some `division`s augur already knows many lat-long coordinates (see which ones it already knows by checking the list [here](https://github.com/nextstrain/augur/blob/master/augur/data/lat_longs.tsv)).
 

diff --git a/docs/faq/seq_traits.md b/docs/faq/seq_traits.md
@@ -1,4 +1,14 @@
 # Inferring Sequence Traits (like Drug Resistance)
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+<!-- WARNING -->
 
 <span style="color:red">Unfortunately this method currently only works with VCF-input files. It will be updated to work with Fasta-input soon!
 

diff --git a/docs/faq/translate_ref.md b/docs/faq/translate_ref.md
@@ -1,4 +1,14 @@
 # Finding a `translate` and `align` reference file
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+<!-- WARNING -->
+<!-- WARNING -->
+<!-- WARNING -->
 
 In order to correctly align and annotate the genes in your sequences, augur uses an annotated reference sequence in 'Genbank' format (if Fasta input) or 'GFF' format (if VCF input).
 
@@ -38,4 +48,4 @@ You can also find an appropriate GFF annotation reference on GenBank. Be sure to
 
 To download a file from GenBank, use the 'send to' button in the top-right corner, then select 'Complete Record', 'File', and 'GFF3' for the format.
 
-You will have to modify the first column of the GFF so that it matches the `CHROM` (first column) of your VCF file.
+You will have to modify the first column of the GFF so that it matches the `CHROM` (first column) of your VCF file.
diff --git a/docs/faq/vcf_input.md b/docs/faq/vcf_input.md
@@ -1,4 +1,14 @@
 # Using VCF Input
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+<!-- WARNING -->
+<!-- WARNING -->
+<!-- WARNING -->
 
 If you would like to run augur on whole-genome bacterial data, you probably would like to start with VCF sequence data. (Note that if you have bacterial SNP data, this may be in Fasta format.)
 
@@ -29,4 +39,4 @@ NC_000962   80194   80623   IG71_Rv0071-Rv0072
 
 _(Optional)_ Bacteria can have thousands of genes, and translating all of them can take quite a bit of time. If you wouldn't like to translate all of them, you can provide a list of genes that you'd like to include in the analysis, and only these will be processed. For example, you might include a list of genes that are associated with drug-resistance. 
 
-To do this, simply create a file with a list of the genes you'd like to include, with one gene name per line. You can then pass this to `augur translate`.
+To do this, simply create a file with a list of the genes you'd like to include, with one gene name per line. You can then pass this to `augur translate`.
diff --git a/docs/installation/installation.md b/docs/installation/installation.md
@@ -1,4 +1,14 @@
 # Installation
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+<!-- WARNING -->
 
 * [Using conda](#using-conda)
 * [Using pip from PyPi](#using-pip-from-pypi)

diff --git a/docs/tutorials/tb_tutorial.md b/docs/tutorials/tb_tutorial.md
@@ -1,4 +1,14 @@
 # MTb tutorials using vcf data
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+<!-- WARNING -->
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+<!-- WARNING -->
 
 This tutorial explains how to create a Nextstrain build for Tuberculosis sequences.
 However, much of it will be applicable to any run where you are starting with [VCF](https://en.wikipedia.org/wiki/Variant_Call_Format) files rather than [FASTA](https://en.wikipedia.org/wiki/FASTA_format) files.

diff --git a/docs/tutorials/zika_tutorial.md b/docs/tutorials/zika_tutorial.md
@@ -1,4 +1,14 @@
 # Zika tutorial -- fasta input
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+<!-- WARNING -->
 
 The tool-chain [*augur*](https://github.com/nextstrain/augur) is the bioinformatics engine of nextstrain and produces the files that can be visualized in the webbrowser using [*auspice*](https://github.com/nextstrain/auspice).
 Augur consists of a number of tools that allow the user to filter and align sequences, build trees, and integrate the phylogenetic analysis with meta data.

diff --git a/docs/usage/augur_snakemake.md b/docs/usage/augur_snakemake.md
@@ -1,4 +1,14 @@
 ## Augur and snakemake
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+<!-- WARNING -->
 
 The output of one augur command serves as input to the next and hence these commands need to be executed in order.
 This is a common pattern in bioinformatics and multiple tools -- so called workflow managers -- exist to facilitate this.