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skchronicles committed Sep 19, 2024
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2 changes: 1 addition & 1 deletion .github/workflows/main.yaml
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Expand Up @@ -18,7 +18,7 @@ jobs:
- name: Dry Run with test data
run: |
docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 \
/opt2/baseline run --input \
/opt2/mutation-seek run --input \
/opt2/.tests/WT_S1.R1.fastq.gz /opt2/.tests/WT_S1.R2.fastq.gz \
/opt2/.tests/WT_S2_R1.fastq.gz /opt2/.tests/WT_S2_R2.fastq.gz \
/opt2/.tests/WT_S3_1.fastq.gz /opt2/.tests/WT_S3_2.fastq.gz \
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46 changes: 23 additions & 23 deletions README.md
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<div align="center">

<h1>baseline 🔬</h1>
<h1>mutation-seek 🔬</h1>

**_long pipeline name_**

[![tests](https://github.com/OpenOmics/baseline/workflows/tests/badge.svg)](https://github.com/OpenOmics/baseline/actions/workflows/main.yaml) [![docs](https://github.com/OpenOmics/baseline/workflows/docs/badge.svg)](https://github.com/OpenOmics/baseline/actions/workflows/docs.yml) [![GitHub issues](https://img.shields.io/github/issues/OpenOmics/baseline?color=brightgreen)](https://github.com/OpenOmics/baseline/issues) [![GitHub license](https://img.shields.io/github/license/OpenOmics/baseline)](https://github.com/OpenOmics/baseline/blob/main/LICENSE)
[![tests](https://github.com/OpenOmics/mutation-seek/workflows/tests/badge.svg)](https://github.com/OpenOmics/mutation-seek/actions/workflows/main.yaml) [![docs](https://github.com/OpenOmics/mutation-seek/workflows/docs/badge.svg)](https://github.com/OpenOmics/mutation-seek/actions/workflows/docs.yml) [![GitHub issues](https://img.shields.io/github/issues/OpenOmics/mutation-seek?color=brightgreen)](https://github.com/OpenOmics/mutation-seek/issues) [![GitHub license](https://img.shields.io/github/license/OpenOmics/mutation-seek)](https://github.com/OpenOmics/mutation-seek/blob/main/LICENSE)

<i>
This is the home of the pipeline, baseline. Its long-term goals: to accurately ...insert goal, to infer ...insert goal, and to boldly ...insert goal like no pipeline before!
This is the home of the pipeline, mutation-seek. Its long-term goals: to accurately ...insert goal, to infer ...insert goal, and to boldly ...insert goal like no pipeline before!
</i>
</div>

## Overview
Welcome to baseline! Before getting started, we highly recommend reading through [baseline's documentation](https://openomics.github.io/baseline/).
Welcome to mutation-seek! Before getting started, we highly recommend reading through [mutation-seek's documentation](https://openomics.github.io/mutation-seek/).

The **`./baseline`** pipeline is composed several inter-related sub commands to setup and run the pipeline across different systems. Each of the available sub commands perform different functions:
The **`./mutation-seek`** pipeline is composed several inter-related sub commands to setup and run the pipeline across different systems. Each of the available sub commands perform different functions:

* [<code>baseline <b>run</b></code>](https://openomics.github.io/baseline/usage/run/): Run the baseline pipeline with your input files.
* [<code>baseline <b>unlock</b></code>](https://openomics.github.io/baseline/usage/unlock/): Unlocks a previous runs output directory.
* [<code>baseline <b>install</b></code>](https://openomics.github.io/baseline/usage/install/): Download reference files locally.
* [<code>baseline <b>cache</b></code>](https://openomics.github.io/baseline/usage/cache/): Cache remote resources locally, coming soon!
* [<code>mutation-seek <b>run</b></code>](https://openomics.github.io/mutation-seek/usage/run/): Run the mutation-seek pipeline with your input files.
* [<code>mutation-seek <b>unlock</b></code>](https://openomics.github.io/mutation-seek/usage/unlock/): Unlocks a previous runs output directory.
* [<code>mutation-seek <b>install</b></code>](https://openomics.github.io/mutation-seek/usage/install/): Download reference files locally.
* [<code>mutation-seek <b>cache</b></code>](https://openomics.github.io/mutation-seek/usage/cache/): Cache remote resources locally, coming soon!

**baseline** is a comprehensive ...insert long description. It relies on technologies like [Singularity<sup>1</sup>](https://singularity.lbl.gov/) to maintain the highest-level of reproducibility. The pipeline consists of a series of data processing and quality-control steps orchestrated by [Snakemake<sup>2</sup>](https://snakemake.readthedocs.io/en/stable/), a flexible and scalable workflow management system, to submit jobs to a cluster.
**mutation-seek** is a comprehensive ...insert long description. It relies on technologies like [Singularity<sup>1</sup>](https://singularity.lbl.gov/) to maintain the highest-level of reproducibility. The pipeline consists of a series of data processing and quality-control steps orchestrated by [Snakemake<sup>2</sup>](https://snakemake.readthedocs.io/en/stable/), a flexible and scalable workflow management system, to submit jobs to a cluster.

The pipeline is compatible with data generated from Illumina short-read sequencing technologies. As input, it accepts a set of FastQ files and can be run locally on a compute instance or on-premise using a cluster. A user can define the method or mode of execution. The pipeline can submit jobs to a cluster using a job scheduler like SLURM (more coming soon!). A hybrid approach ensures the pipeline is accessible to all users.

Before getting started, we highly recommend reading through the [usage](https://openomics.github.io/baseline/usage/run/) section of each available sub command.
Before getting started, we highly recommend reading through the [usage](https://openomics.github.io/mutation-seek/usage/run/) section of each available sub command.

For more information about issues or trouble-shooting a problem, please checkout our [FAQ](https://openomics.github.io/baseline/faq/questions/) prior to [opening an issue on Github](https://github.com/OpenOmics/baseline/issues).
For more information about issues or trouble-shooting a problem, please checkout our [FAQ](https://openomics.github.io/mutation-seek/faq/questions/) prior to [opening an issue on Github](https://github.com/OpenOmics/mutation-seek/issues).

## Dependencies
**Requires:** `singularity>=3.5` `snakemake>=6.0`
**Requires:** `singularity>=3.5` `snakemake>=6.0` `snakemake<8.0`

At the current moment, the pipeline uses a mixture of enviroment modules and docker images; however, this will be changing soon! In the very near future, the pipeline will only use docker images. With that being said, [snakemake](https://snakemake.readthedocs.io/en/stable/getting_started/installation.html) and [singularity](https://singularity.lbl.gov/all-releases) must be installed on the target system. Snakemake orchestrates the execution of each step in the pipeline. To guarantee the highest level of reproducibility, each step of the pipeline will rely on versioned images from [DockerHub](https://hub.docker.com/orgs/nciccbr/repositories). Snakemake uses singularity to pull these images onto the local filesystem prior to job execution, and as so, snakemake and singularity will be the only two dependencies in the future.

## Installation
Please clone this repository to your local filesystem using the following command:
```bash
# Clone Repository from Github
git clone https://github.com/OpenOmics/baseline.git
git clone https://github.com/OpenOmics/mutation-seek.git
# Change your working directory
cd baseline/
cd mutation-seek/
# Add dependencies to $PATH
# Biowulf users should run
module load snakemake singularity
# Get usage information
./baseline -h
./mutation-seek -h
```

## Contribute
This site is a living document, created for and by members like you. baseline is maintained by the members of OpenOmics and is improved by continous feedback! We encourage you to contribute new content and make improvements to existing content via pull request to our [GitHub repository](https://github.com/OpenOmics/baseline).
This site is a living document, created for and by members like you. mutation-seek is maintained by the members of OpenOmics and is improved by continous feedback! We encourage you to contribute new content and make improvements to existing content via pull request to our [GitHub repository](https://github.com/OpenOmics/mutation-seek).


## Cite
Expand All @@ -75,7 +75,7 @@ Citation coming soon!
</details>

<!---
# Setup from baseline template
# Setup from mutation-seek template
```bash
# Add your new pipeline name here,
# whatever you set here will be the
Expand All @@ -87,18 +87,18 @@ new_pipeline_name="add_your_pipeline_name_here"
# Dry-run: This step automagically builds a
# command to update any instances of the string
# baseline with your new pipeline name, please
# mutation-seek with your new pipeline name, please
# make sure to set the variable above to whatever
# you want to name the pipeline and CLI.
find . -type f -not -path '*/.baseline_version' -not -path '*./CHANGELOG.md' -not -path '*/.git/*' -exec grep 'baseline' {} /dev/null \; | awk -F ':' '{print $1}' | sort | uniq | sed "s/^/sed -i 's@baseline@$new_pipeline_name@g' /g"
find . -type f -not -path '*/.mutation-seek_version' -not -path '*./CHANGELOG.md' -not -path '*/.git/*' -exec grep 'mutation-seek' {} /dev/null \; | awk -F ':' '{print $1}' | sort | uniq | sed "s/^/sed -i 's@mutation-seek@$new_pipeline_name@g' /g"
# Updates any instances of the string baseline
# Updates any instances of the string mutation-seek
# with the name you decided/set above.
find . -type f -not -path '*/.baseline_version' -not -path '*./CHANGELOG.md' -not -path '*/.git/*' -exec grep 'baseline' {} /dev/null \; | awk -F ':' '{print $1}' | sort | uniq | sed "s/^/sed -i 's@baseline@$new_pipeline_name@g' /g" | bash
find . -type f -not -path '*/.mutation-seek_version' -not -path '*./CHANGELOG.md' -not -path '*/.git/*' -exec grep 'mutation-seek' {} /dev/null \; | awk -F ':' '{print $1}' | sort | uniq | sed "s/^/sed -i 's@mutation-seek@$new_pipeline_name@g' /g" | bash
# Rename the cli or main entry point
# of the pipeline
mv baseline "$new_pipeline_name"
mv mutation-seek "$new_pipeline_name"
```
-->

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8 changes: 4 additions & 4 deletions baseline
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Expand Up @@ -25,9 +25,9 @@ merchantability or fitness for any particular purpose.
Please cite the author and NIH resources like the "Biowulf Cluster"
in any work or product based on this material.
USAGE:
$ baseline <command> [OPTIONS]
$ mutation-seek <command> [OPTIONS]
EXAMPLE:
$ baseline run --input *.R?.fastq.gz --output output/
$ mutation-seek run --input *.R?.fastq.gz --output output/
"""

# Python standard library
Expand Down Expand Up @@ -58,7 +58,7 @@ __authors__ = 'Skyler Kuhn'
__email__ = '[email protected]'
__home__ = os.path.dirname(os.path.abspath(__file__))
_name = os.path.basename(sys.argv[0])
_description = 'An awesome baseline pipeline'
_description = 'An awesome mutation-seek pipeline'


def unlock(sub_args):
Expand Down Expand Up @@ -217,7 +217,7 @@ def parsed_arguments(name, description):
"""
# Add styled name and description
c = Colors
styled_name = "{0}{1}{2}baseline{3}".format(c.bold, c.bg_black, c.cyan, c.end)
styled_name = "{0}{1}{2}mutation-seek{3}".format(c.bold, c.bg_black, c.cyan, c.end)
description = "{0}{1}{2}".format(c.bold, description, c.end)

# Create a top-level parser
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6 changes: 3 additions & 3 deletions docs/README.md
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# Build documentation

> **Please Note:** When a commit is pushed to the `docs/` directory, it triggers a [github actions workflow](https://github.com/OpenOmics/baseline/actions) to build the static-site and push it to the gh-pages branch.
> **Please Note:** When a commit is pushed to the `docs/` directory, it triggers a [github actions workflow](https://github.com/OpenOmics/mutation-seek/actions) to build the static-site and push it to the gh-pages branch.
### Installation
```bash
# Clone the Repository
git clone https://github.com/OpenOmics/baseline.git
cd baseline/
git clone https://github.com/OpenOmics/mutation-seek.git
cd mutation-seek/
# Create a virtual environment
python3 -m venv .venv
# Activate the virtual environment
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2 changes: 1 addition & 1 deletion docs/faq/questions.md
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# Frequently Asked Questions

This page is still under construction. If you need immediate help, please [open an issue](https://github.com/OpenOmics/baseline/issues) on Github!
This page is still under construction. If you need immediate help, please [open an issue](https://github.com/OpenOmics/mutation-seek/issues) on Github!

40 changes: 20 additions & 20 deletions docs/index.md
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<div align="center">

<h1 style="font-size: 250%">baseline 🔬</h1>
<h1 style="font-size: 250%">mutation-seek 🔬</h1>

<b><i>long pipeline name</i></b><br>
<a href="https://github.com/OpenOmics/baseline/actions/workflows/main.yaml">
<img alt="tests" src="https://github.com/OpenOmics/baseline/workflows/tests/badge.svg">
<a href="https://github.com/OpenOmics/mutation-seek/actions/workflows/main.yaml">
<img alt="tests" src="https://github.com/OpenOmics/mutation-seek/workflows/tests/badge.svg">
</a>
<a href="https://github.com/OpenOmics/baseline/actions/workflows/docs.yml">
<img alt="docs" src="https://github.com/OpenOmics/baseline/workflows/docs/badge.svg">
<a href="https://github.com/OpenOmics/mutation-seek/actions/workflows/docs.yml">
<img alt="docs" src="https://github.com/OpenOmics/mutation-seek/workflows/docs/badge.svg">
</a>
<a href="https://github.com/OpenOmics/baseline/issues">
<img alt="GitHub issues" src="https://img.shields.io/github/issues/OpenOmics/baseline?color=brightgreen">
<a href="https://github.com/OpenOmics/mutation-seek/issues">
<img alt="GitHub issues" src="https://img.shields.io/github/issues/OpenOmics/mutation-seek?color=brightgreen">
</a>
<a href="https://github.com/OpenOmics/baseline/blob/main/LICENSE">
<img alt="GitHub license" src="https://img.shields.io/github/license/OpenOmics/baseline">
<a href="https://github.com/OpenOmics/mutation-seek/blob/main/LICENSE">
<img alt="GitHub license" src="https://img.shields.io/github/license/OpenOmics/mutation-seek">
</a>

<p>
This is the home of the pipeline, baseline. Its long-term goals: to accurately ...insert goal, to infer ...insert goal, and to boldly ...insert goal like no pipeline before!
This is the home of the pipeline, mutation-seek. Its long-term goals: to accurately ...insert goal, to infer ...insert goal, and to boldly ...insert goal like no pipeline before!
</p>

</div>


## Overview
Welcome to baseline's documentation! This guide is the main source of documentation for users that are getting started with the [long pipeline name](https://github.com/OpenOmics/baseline/).
Welcome to mutation-seek's documentation! This guide is the main source of documentation for users that are getting started with the [long pipeline name](https://github.com/OpenOmics/mutation-seek/).

The **`./baseline`** pipeline is composed several inter-related sub commands to setup and run the pipeline across different systems. Each of the available sub commands perform different functions:
The **`./mutation-seek`** pipeline is composed several inter-related sub commands to setup and run the pipeline across different systems. Each of the available sub commands perform different functions:

<section align="center" markdown="1" style="display: flex; flex-wrap: row wrap; justify-content: space-around;">

!!! inline custom-grid-button ""

[<code style="font-size: 1em;">baseline <b>run</b></code>](usage/run.md)
Run the baseline pipeline with your input files.
[<code style="font-size: 1em;">mutation-seek <b>run</b></code>](usage/run.md)
Run the mutation-seek pipeline with your input files.

!!! inline custom-grid-button ""

[<code style="font-size: 1em;">baseline <b>unlock</b></code>](usage/unlock.md)
[<code style="font-size: 1em;">mutation-seek <b>unlock</b></code>](usage/unlock.md)
Unlocks a previous runs output directory.

</section>
Expand All @@ -47,28 +47,28 @@ The **`./baseline`** pipeline is composed several inter-related sub commands to

!!! inline custom-grid-button ""

[<code style="font-size: 1em;">baseline <b>install</b></code>](usage/install.md)
[<code style="font-size: 1em;">mutation-seek <b>install</b></code>](usage/install.md)
Download remote reference files locally.


!!! inline custom-grid-button ""

[<code style="font-size: 1em;">baseline <b>cache</b></code>](usage/cache.md)
[<code style="font-size: 1em;">mutation-seek <b>cache</b></code>](usage/cache.md)
Cache remote software containers locally.

</section>

**baseline** is a comprehensive ...insert long description. It relies on technologies like [Singularity<sup>1</sup>](https://singularity.lbl.gov/) to maintain the highest-level of reproducibility. The pipeline consists of a series of data processing and quality-control steps orchestrated by [Snakemake<sup>2</sup>](https://snakemake.readthedocs.io/en/stable/), a flexible and scalable workflow management system, to submit jobs to a cluster.
**mutation-seek** is a comprehensive ...insert long description. It relies on technologies like [Singularity<sup>1</sup>](https://singularity.lbl.gov/) to maintain the highest-level of reproducibility. The pipeline consists of a series of data processing and quality-control steps orchestrated by [Snakemake<sup>2</sup>](https://snakemake.readthedocs.io/en/stable/), a flexible and scalable workflow management system, to submit jobs to a cluster.

The pipeline is compatible with data generated from Illumina short-read sequencing technologies. As input, it accepts a set of FastQ files and can be run locally on a compute instance or on-premise using a cluster. A user can define the method or mode of execution. The pipeline can submit jobs to a cluster using a job scheduler like SLURM (more coming soon!). A hybrid approach ensures the pipeline is accessible to all users.

Before getting started, we highly recommend reading through the [usage](usage/run.md) section of each available sub command.

For more information about issues or trouble-shooting a problem, please checkout our [FAQ](faq/questions.md) prior to [opening an issue on Github](https://github.com/OpenOmics/baseline/issues).
For more information about issues or trouble-shooting a problem, please checkout our [FAQ](faq/questions.md) prior to [opening an issue on Github](https://github.com/OpenOmics/mutation-seek/issues).

## Contribute

This site is a living document, created for and by members like you. baseline is maintained by the members of NCBR and is improved by continous feedback! We encourage you to contribute new content and make improvements to existing content via pull request to our [GitHub repository :octicons-heart-fill-24:{ .heart }](https://github.com/OpenOmics/baseline).
This site is a living document, created for and by members like you. mutation-seek is maintained by the members of NCBR and is improved by continous feedback! We encourage you to contribute new content and make improvements to existing content via pull request to our [GitHub repository :octicons-heart-fill-24:{ .heart }](https://github.com/OpenOmics/mutation-seek).

## Citation

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