DNA Snakemake Proto-Workflow

Setup

Check the complete and official Snakemake Tutorial.

Step 1: Installing Miniconda 3

The easiest way to setup these prerequisites is to use the Miniconda Python 3 distribution.

$ wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
$ bash Miniconda3-latest-Linux-x86_64.sh

Answer yes. Along with a minimal Python 3 environment, Miniconda contains the package manager Conda. After opening a new terminal, you can use the new conda command to install software packages and create isolated environments to, e.g. Later you'll see how to create an enviroment.

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Reproduce results

1. Clone this repository into your machine:

git clone https://github.com/mv-lab/dna-proto-workflow.git

Check the new directory

cd dna-proto-workflow
ls

2. Creating an environment with the required software

NOTE: conda's enviroment name in these examples is snkmk.

$ conda env create --name snkmk --file envs/condaenv.yml

3. Activate the enviroment using:

$ conda activate snkmk

Check this conda cheatsheet for more useful commands and tricks.

Now you are ready to run Snakemake.

NOTE: the output directory and metadata files are generated by the workflow.

get dag.svg and check rules (see --dag -npr)

snakemake --dag -npr -j -1 | dot -Tsvg > dag.svg
eog dag.svg

Run complete Workflow

snakemake  -npr -j -1

Check config and metadata

utils/check_config.py allows you to read and print the config files:

from utils.check_config import *
config = readconfig('config.yml')
pconfig(config)
config['qc']

utils/check_metadata.py allows you to print the metadata generated at the common rule:

python utils/check_metadata.py

Data

Main directory content:

.
├── config.yml
├── envs
├── genomes_and_annotations
├── metadata
├── output
├── rules
├── samples
├── scripts
├── Snakefile
├── snpEff.config
├── utils
├── ...

The workflow uses the data from the following folders:

• genomes_and_annotations
• samples

You can download example data for testing the workflow. click here to download

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How to contribute

Fork this repository

Fork this repository by clicking on the fork button on the top of this page. This will create a copy of this repository in your GitHub account (not in your computer).

Clone the repository

Now clone the forked repository to your machine. Go to your GitHub account, open the forked repository, click on the clone button and then click the copy to clipboard icon. The url is going to be like: https://github.com/your-username/dna-proto-workflow.git where your-username is your GitHub username.

Open a terminal and run the following git command:

git clone https://github.com/your-username/dna-proto-workflow.git

Once you've cloned your fork, you can edit your local copy. However, if you want to contribute, you'll need to create a new branch as follows.

Create a branch

Change to the repository directory on your computer (if you are not already there):

NOTE: you can't change the name of the directory.

cd dna-proto-workflow

You can check your branches and what branch you're currently in, using the git branch command.

Now create a branch using the git checkout command:

git checkout -b new-branch-name

For example:

git checkout -b development

From this point, you are in the new branch If something goes wrong, you can remove a branch using git branch -d name-of-the-branch. Or you can go back to the masterbranch using git checkout master.

Make changes and commit

Once you modify something, if you go to the project directory and execute the command git status, you'll see there are changes. Add those changes to your branch using the git add command:

git add .
or
git add name_of_the_file_you_modified

Now commit those changes using the git commit command:

git commit -m "write a message"

Push changes to GitHub

Push your changes from your local copy (in your machine) to your Github (remote repository) using the command git push:

git push origin your-branch-name

replacing your-branch-name with the name of the branch you created earlier (eg development).

Submit your changes for review

If you go to your repository on GitHub, you'll see a Compare & pull request button. Click on that button.

Now submit the pull request and you'll see something like:

We'll check your changes and merge them into this project (in general, into the master branch). You will get a notification email once the changes have been merged :)