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README.md

@@ -6,7 +6,7 @@ A pipeline for running an ensemble of variant callers to predict variants in ATA
 
 The entire pipeline is made up of two smaller subworkflows. The `prepare` subworkflow calls each variant caller and prepares the resulting data for use by the `classify` subworkflow, which runs the ensemble classifier to predict the existence of variants at each site.
 
-# Download
+# download
 Execute the following command or download the [latest release](https://github.com/aryam7/varCA/releases/latest) manually.
 ```
 git clone https://github.com/aryam7/varCA.git
@@ -17,16 +17,15 @@ cd varCA
 wget -O- -q https://github.com/aryam7/varCA/releases/latest/download/data.tar.gz | tar xvzf -
 ```
 
-# Setup
-We highly recommend you install [Snakemake via conda](https://snakemake.readthedocs.io/en/stable/getting_started/installation.html#installation-via-conda) so that you can use the `--use-conda` flag when calling `snakemake` to let it automatically handle all dependencies of the pipeline. Otherwise, you must manually install the dependencies listed in the [env files](envs).
-
-We recommend installing version 5.18.0
+# setup
+The pipeline is written as a Snakefile, so it must be executed via [Snakemake](https://snakemake.readthedocs.io). We recommend installing version 5.18.0:
 ```
 conda create -n snakemake -c bioconda -c conda-forge 'snakemake==5.18.0'
 ```
+We highly recommend you install [Snakemake via conda](https://snakemake.readthedocs.io/en/stable/getting_started/installation.html#installation-via-conda) like this so that you can use the `--use-conda` flag when calling `snakemake` to let it [automatically handle all dependencies](https://snakemake.readthedocs.io/en/stable/snakefiles/deployment.html#integrated-package-management) of the pipeline. Otherwise, you must manually install the dependencies listed in the [env files](envs).
 
-# Execution
-1. Activate snakemake via `conda`
+# execution
+1. Activate snakemake via `conda`:
     ```
     conda activate snakemake
     ```
@@ -36,14 +35,14 @@ conda create -n snakemake -c bioconda -c conda-forge 'snakemake==5.18.0'
     ```
     ./run.bash &
     ```
-    or on an SGE cluster:
+    __or__ on an SGE cluster:
     ```
     ./run.bash --sge-cluster &
     ```
 
-The pipeline is written as a Snakefile, so it must be executed via [Snakemake](https://snakemake.readthedocs.io). If you want to execute the pipeline on your own data, you must provide [required input in the config.yaml file](configs#configyaml) before executing. This config file is currently configured to run the pipeline on the example data provided.
+If you want to execute the pipeline on your own data, you must provide [required input in the config.yaml file](configs#configyaml) first. The config file is currently configured to run the pipeline on the example data provided.
 
-The pipeline is made up of [two subworkflows](rules), which can each be executed separately from the master pipeline for more advanced usage. See the [rules README](rules/README.md) for execution instructions. You will need to execute the subworkflows separately [if you ever need to create your own trained models](rules#creating-your-own-trained-model).
+The pipeline is made up of [two subworkflows](rules), which can each be executed on their own for more advanced usage. See the [rules README](rules/README.md) for execution instructions. You will need to execute the subworkflows separately [if you ever want to create your own trained models](rules#training-and-testing-varca).
 
 ### If this is your first time using Snakemake
 We highly recommend that you run `snakemake --help` to learn about all of the options available to you. You might discover, for example, that calling Snakemake with the `-n -p -r` flags can be a helpful way to check that the pipeline will be executed correctly before you run it. This can also be a good way to familiarize yourself with the steps of the pipeline and their inputs and outputs (the latter of which are inputs to the first rule in each workflow -- ie the `all` rule).
@@ -52,7 +51,7 @@ Another important thing to know is that Snakemake will not recreate output that
 
 By default, the pipeline will automatically delete some files it deems unnecessary (ex: unsorted copies of a BAM). You can opt to keep these files instead by providing the `--notemp` flag to Snakemake when executing the pipeline.
 
-# Files and Directories
+# files and directories
 
 ### [Snakefile](Snakefile)
 A [Snakemake](https://snakemake.readthedocs.io/en/stable/) pipeline for calling variants from a set of ATAC-seq reads. This pipeline is made up of two subworkflows:
@@ -76,4 +75,4 @@ Scripts for calculating posterior probabilities for the existence of an insertio
 Various scripts used by the pipeline. See the [script README](scripts/README.md) for more information.
 
 ### [run.bash](run.bash)
-An example bash script for executing the pipeline using `snakemake` and `conda`. Any parameters to this script are passed directly to `snakemake`.
+An example bash script for executing the pipeline using `snakemake` and `conda`. Any arguments to this script are passed directly to `snakemake`.