From 48b9a5a43a9b5903bccb384644cb47f0899dfb07 Mon Sep 17 00:00:00 2001 From: Arya Massarat <23412689+aryam7@users.noreply.github.com> Date: Thu, 2 Jul 2020 15:34:16 -0700 Subject: [PATCH] revert to lowercase titles they just look much more gentle and less intimidating --- README.md | 23 +++++++++++------------ 1 file changed, 11 insertions(+), 12 deletions(-) diff --git a/README.md b/README.md index b400798..05437e7 100644 --- a/README.md +++ b/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`.