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<ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>

<li class="md-nav__item">
<a href="#environment-seteup" class="md-nav__link">
<a href="#environment-setup" class="md-nav__link">
<span class="md-ellipsis">
Environment Seteup
Environment Setup
</span>
</a>

<nav class="md-nav" aria-label="Environment Seteup">
<nav class="md-nav" aria-label="Environment Setup">
<ul class="md-nav__list">

<li class="md-nav__item">
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</li>

<li class="md-nav__item">
<a href="#2-install-mamba" class="md-nav__link">
<a href="#2-install-mamba-and-add-it-to-your-path" class="md-nav__link">
<span class="md-ellipsis">
(2) Install mamba:
(2) Install mamba and add it to your PATH
</span>
</a>

</li>

<li class="md-nav__item">
<a href="#3-add-mamba-to-path" class="md-nav__link">
<a href="#3-create-and-activate-a-conda-environment" class="md-nav__link">
<span class="md-ellipsis">
(3) Add mamba to PATH:
(3) Create and activate a conda environment
</span>
</a>

</li>

<li class="md-nav__item">
<a href="#4-create-the-conda-environment" class="md-nav__link">
<a href="#4-install-nextflow-using-mamba-and-the-bioconda-channel" class="md-nav__link">
<span class="md-ellipsis">
(4) Create the conda environment:
(4) Install Nextflow using mamba and the bioconda Channel
</span>
</a>

<nav class="md-nav" aria-label="(4) Create the conda environment:">
<nav class="md-nav" aria-label="(4) Install Nextflow using mamba and the bioconda Channel">
<ul class="md-nav__list">

<li class="md-nav__item">
<a href="#4a-create-the-conda-environment-and-install-the-dependencies-set-in-your-environmentyml" class="md-nav__link">
<a href="#install-nextflow" class="md-nav__link">
<span class="md-ellipsis">
(4a) Create the conda environment and install the dependencies set in your environment.yml:
Install Nextflow
</span>
</a>

</li>

<li class="md-nav__item">
<a href="#4b-create-an-empty-conda-environment" class="md-nav__link">
<a href="#ensure-installation-was-successful-by-running-nextflow-with-the-v-or-version-flag" class="md-nav__link">
<span class="md-ellipsis">
(4b) Create an empty conda environment:
Ensure installation was successful by running nextflow with the -v or -version flag
</span>
</a>

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</li>

<li class="md-nav__item">
<a href="#5-activate-the-environment" class="md-nav__link">
<a href="#5-update-the-default-submissions-config-file-with-your-ncbi-username-and-password-and-run-the-following-nextflow-command-to-execute-the-scripts-with-default-parameters-and-the-local-run-environment" class="md-nav__link">
<span class="md-ellipsis">
(5) Activate the environment.
</span>
</a>

</li>

<li class="md-nav__item">
<a href="#6-install-nextflow-using-use-mamba-and-the-bioconda-channel" class="md-nav__link">
<span class="md-ellipsis">
(6) Install Nextflow using Use Mamba and the Bioconda Channel:
</span>
</a>

</li>

<li class="md-nav__item">
<a href="#7-ensure-nextflow-was-installed-successfully-by-running-nextflow-v" class="md-nav__link">
<span class="md-ellipsis">
(7) Ensure Nextflow was installed successfully by running nextflow -v
</span>
</a>

</li>

<li class="md-nav__item">
<a href="#8-run-one-of-the-following-nextflow-commands-to-execute-the-scripts-with-default-parameters-and-the-local-run-environment" class="md-nav__link">
<span class="md-ellipsis">
(8) Run one of the following nextflow commands to execute the scripts with default parameters and the local run environment:
(5) Update the default submissions config file with your NCBI username and password, and run the following nextflow command to execute the scripts with default parameters and the local run environment:
</span>
</a>

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<ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>

<li class="md-nav__item">
<a href="#environment-seteup" class="md-nav__link">
<a href="#environment-setup" class="md-nav__link">
<span class="md-ellipsis">
Environment Seteup
Environment Setup
</span>
</a>

<nav class="md-nav" aria-label="Environment Seteup">
<nav class="md-nav" aria-label="Environment Setup">
<ul class="md-nav__list">

<li class="md-nav__item">
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</li>

<li class="md-nav__item">
<a href="#2-install-mamba" class="md-nav__link">
<a href="#2-install-mamba-and-add-it-to-your-path" class="md-nav__link">
<span class="md-ellipsis">
(2) Install mamba:
(2) Install mamba and add it to your PATH
</span>
</a>

</li>

<li class="md-nav__item">
<a href="#3-add-mamba-to-path" class="md-nav__link">
<a href="#3-create-and-activate-a-conda-environment" class="md-nav__link">
<span class="md-ellipsis">
(3) Add mamba to PATH:
(3) Create and activate a conda environment
</span>
</a>

</li>

<li class="md-nav__item">
<a href="#4-create-the-conda-environment" class="md-nav__link">
<a href="#4-install-nextflow-using-mamba-and-the-bioconda-channel" class="md-nav__link">
<span class="md-ellipsis">
(4) Create the conda environment:
(4) Install Nextflow using mamba and the bioconda Channel
</span>
</a>

<nav class="md-nav" aria-label="(4) Create the conda environment:">
<nav class="md-nav" aria-label="(4) Install Nextflow using mamba and the bioconda Channel">
<ul class="md-nav__list">

<li class="md-nav__item">
<a href="#4a-create-the-conda-environment-and-install-the-dependencies-set-in-your-environmentyml" class="md-nav__link">
<a href="#install-nextflow" class="md-nav__link">
<span class="md-ellipsis">
(4a) Create the conda environment and install the dependencies set in your environment.yml:
Install Nextflow
</span>
</a>

</li>

<li class="md-nav__item">
<a href="#4b-create-an-empty-conda-environment" class="md-nav__link">
<a href="#ensure-installation-was-successful-by-running-nextflow-with-the-v-or-version-flag" class="md-nav__link">
<span class="md-ellipsis">
(4b) Create an empty conda environment:
Ensure installation was successful by running nextflow with the -v or -version flag
</span>
</a>

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</li>

<li class="md-nav__item">
<a href="#5-activate-the-environment" class="md-nav__link">
<span class="md-ellipsis">
(5) Activate the environment.
</span>
</a>

</li>

<li class="md-nav__item">
<a href="#6-install-nextflow-using-use-mamba-and-the-bioconda-channel" class="md-nav__link">
<span class="md-ellipsis">
(6) Install Nextflow using Use Mamba and the Bioconda Channel:
</span>
</a>

</li>

<li class="md-nav__item">
<a href="#7-ensure-nextflow-was-installed-successfully-by-running-nextflow-v" class="md-nav__link">
<a href="#5-update-the-default-submissions-config-file-with-your-ncbi-username-and-password-and-run-the-following-nextflow-command-to-execute-the-scripts-with-default-parameters-and-the-local-run-environment" class="md-nav__link">
<span class="md-ellipsis">
(7) Ensure Nextflow was installed successfully by running nextflow -v
</span>
</a>

</li>

<li class="md-nav__item">
<a href="#8-run-one-of-the-following-nextflow-commands-to-execute-the-scripts-with-default-parameters-and-the-local-run-environment" class="md-nav__link">
<span class="md-ellipsis">
(8) Run one of the following nextflow commands to execute the scripts with default parameters and the local run environment:
(5) Update the default submissions config file with your NCBI username and password, and run the following nextflow command to execute the scripts with default parameters and the local run environment:
</span>
</a>

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<h1 id="installation">Installation</h1>
<h2 id="environment-seteup">Environment Seteup</h2>
<h2 id="environment-setup">Environment Setup</h2>
<h3 id="dependencies">Dependencies:</h3>
<ul>
<li>Nextflow v. 21.01.03</li>
<li>Nextflow v. 21.01.03 or newer</li>
<li>Compute environment (docker, singularity or conda)
❗ Note: If you are a CDC user, please follow the set-up instructions found on this page: CDC User Guide</li>
❗ Note: If you are a CDC user, please follow the set-up instructions found on this page: <a href="https://github.com/CDCgov/tostadas/wiki/CDC-User-Guide">CDC User Guide</a></li>
</ul>
<h3 id="1-clone-the-repository-to-your-local-machine">(1) Clone the repository to your local machine:</h3>
<ul>
<li><code>git clone https://github.com/CDCgov/tostadas.git</code>
❗ Note: If you have mamba or nextflow installed in your local environment, you may skip steps 2, 3 (mamba installation) and 6 (nextflow installation) accordingly.</li>
</ul>
<h3 id="2-install-mamba">(2) Install mamba:</h3>
<ul>
<li><code>curl -L -O https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(uname)-$(uname -m).sh</code></li>
<li><code>bash Mambaforge-$(uname)-$(uname -m).sh -b -p $HOME/mambaforge</code></li>
</ul>
<h3 id="3-add-mamba-to-path">(3) Add mamba to PATH:</h3>
<ul>
<li><code>export PATH="$HOME/mambaforge/bin:$PATH"</code></li>
</ul>
<h3 id="4-create-the-conda-environment">(4) Create the conda environment:</h3>
<p>If you want to create the full-conda environment needed to run the pipeline outside of Nextflow (this enables you to run individual python scripts), then proceed with step 4a.</p>
<p>If you want to run the pipeline using nextflow only (this will be most users), proceed with step 4b. Nextflow will handle environment creation and you would only need to install the nextflow package locally vs the entire environment.</p>
<h4 id="4a-create-the-conda-environment-and-install-the-dependencies-set-in-your-environmentyml">(4a) Create the conda environment and install the dependencies set in your environment.yml:</h4>
<ul>
<li><code>cd tostadas</code></li>
<li><code>mamba env create -n tostadas -f environment.yml</code> </li>
</ul>
<h4 id="4b-create-an-empty-conda-environment">(4b) Create an empty conda environment:</h4>
<ul>
<li><code>conda create --name tostadas</code>
This conda environment will be used to install Nextflow.</li>
</ul>
<h3 id="5-activate-the-environment">(5) Activate the environment.</h3>
<ul>
<li><code>conda activate tostadas</code>
Verify which environment is active by running the following conda command: <code>conda env list</code>. The active environment will be denoted with an asterisk <code>*</code></li>
</ul>
<h3 id="6-install-nextflow-using-use-mamba-and-the-bioconda-channel">(6) Install Nextflow using Use Mamba and the Bioconda Channel:</h3>
<ul>
<li><code>mamba install -c bioconda nextflow</code>
❗ Optionally, you may install nextflow without mamba by following the instructions found in the Nextflow Installation Documentation Page: <a href="https://www.nextflow.io/docs/latest/getstarted.html">Nextflow Install</a></li>
</ul>
<h3 id="7-ensure-nextflow-was-installed-successfully-by-running-nextflow-v">(7) Ensure Nextflow was installed successfully by running <code>nextflow -v</code></h3>
<p>Expected output:</p>
<ul>
<li><code>nextflow version &lt;CURRENT VERSION&gt;</code>
The exact version of Nextflow returned will differ from installation to installation. It is important that the command executes successfully, and a version number is returned.</li>
</ul>
<h3 id="8-run-one-of-the-following-nextflow-commands-to-execute-the-scripts-with-default-parameters-and-the-local-run-environment">(8) Run one of the following nextflow commands to execute the scripts with default parameters and the local run environment:</h3>
<ul>
<li><code># for virus reads</code></li>
<li><code>nextflow run main.nf -profile test,&lt;singularity/docker/conda&gt; --virus</code></li>
<li><code># for bacterial reads</code></li>
<li><code>nextflow run main.nf -profile test,&lt;singularity/docker/conda&gt; --bacteria</code></li>
</ul>
<p>The outputs of the pipeline will appear in the <code>test_output</code> folder within the project directory. You can specify an output directory in the config file or by supplying a path to the <code>--output_dir</code> flag in your nextflow run command.</p>
<h3 id="2-install-mamba-and-add-it-to-your-path">(2) Install mamba and add it to your PATH</h3>
<p>2a. Install mamba</p>
<p>❗ Note: If you have mamba installed in your local environment, skip ahead to step 3 (Create and activate a conda environment)</p>
<p><code>curl -L -O https://github.com/conda-forge/miniforge/releases/latest/download</code>
<code>Mambaforge-$(uname)-$(uname -m).sh</code>
<code>bash Mambaforge-$(uname)-$(uname -m).sh -b -p $HOME/mambaforge</code>
2b. Add mamba to PATH:</p>
<p><code>export PATH="$HOME/mambaforge/bin:$PATH"</code></p>
<h3 id="3-create-and-activate-a-conda-environment">(3) Create and activate a conda environment</h3>
<p>3a. Create an empty conda environment to install Nextflow into</p>
<p><code>conda create --name tostadas</code>
3b. Activate the environment</p>
<p><code>conda activate tostadas</code>
Verify which environment is active by running the following conda command: <code>conda env list</code>. The active environment will be denoted with an asterisk <code>*</code></p>
<h3 id="4-install-nextflow-using-mamba-and-the-bioconda-channel">(4) Install Nextflow using mamba and the bioconda Channel</h3>
<h4 id="install-nextflow">Install Nextflow</h4>
<p><code>mamba install -c bioconda nextflow</code></p>
<h4 id="ensure-installation-was-successful-by-running-nextflow-with-the-v-or-version-flag">Ensure installation was successful by running nextflow with the -v or -version flag</h4>
<p><code>nextflow -v</code>
Expected output:</p>
<p><code>nextflow version &lt;CURRENT VERSION&gt;</code>
The exact version of Nextflow returned will differ from installation to installation. It is important that the command executes successfully, and a version number is returned.</p>
<h3 id="5-update-the-default-submissions-config-file-with-your-ncbi-username-and-password-and-run-the-following-nextflow-command-to-execute-the-scripts-with-default-parameters-and-the-local-run-environment">(5) Update the default submissions config file with your NCBI username and password, and run the following nextflow command to execute the scripts with default parameters and the local run environment:</h3>
<p><code># update this config file (you don't have to use vim)</code>
<code>vim bin/config_files/default_config.yaml</code>
<code># for virus reads</code>
<code>nextflow run main.nf -profile test,&lt;singularity|docker|conda&gt; --virus</code>
❗ Note: If you do not update the default_config.yaml file with your NCBI credentials, you will see the following command error: <code>Error:530 Login incorrect</code>.</p>
<p>The outputs of the pipeline will appear in the test_output folder within the project directory. You can specify an output directory in the config file or by supplying a path to the <code>--output_dir</code> flag in your <code>nextflow run</code> command.</p>



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