https://github.com/fpsom/metagenomics-pipeline
https://github.com/fpsom/metagenomics-pipeline
Last synced: 5 months ago
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- Host: GitHub
- URL: https://github.com/fpsom/metagenomics-pipeline
- Owner: fpsom
- License: gpl-3.0
- Created: 2019-07-12T09:47:56.000Z (almost 7 years ago)
- Default Branch: master
- Last Pushed: 2019-09-23T11:13:51.000Z (over 6 years ago)
- Last Synced: 2025-05-21T11:15:01.018Z (about 1 year ago)
- Language: Common Workflow Language
- Size: 61.5 KB
- Stars: 0
- Watchers: 0
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Metagenomics - Pipeline
In this project we built a metagenomics-pipeline.
## Getting Started
These instructions will get you a copy of the project up and running on your local machine for development and testing purposes.
### Prerequisites
Qiime2 does not currently support Windows.
In case a windows platform is required, we recommend using [Windows Subsystem for Linux](https://docs.microsoft.com/en-us/windows/wsl/install-win10) or [Virtual Machines](https://docs.qiime2.org/2019.7/install/virtual/)
### Installing
Download and install the latest version of [miniconda](https://docs.conda.io/en/latest/miniconda.html):
```
curl -O -L https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh
```
Add the correct channels in the conda (so that it knows where to look for packages):
```
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
```
Install (and activate) [Qiime2](https://docs.qiime2.org/2019.7/install/native/) within a ```conda``` enviroment:
```
wget https://data.qiime2.org/distro/core/qiime2-2019.7-py36-linux-conda.yml
conda env create -n qiime2-2019.7 --file qiime2-2019.7-py36-linux-conda.yml
```
Install [CWL tool](https://github.com/common-workflow-language/cwltool) into Qiime2 enviroment:
```
conda install -c bioconda cwltool
```
Install required tools into Qiime2 enviroment:
```
conda install -c bioconda fastqc trim-galore
```
In case R is not installed in Qiime2 enviroment, please follow the instructions found here: https://cran.r-project.org/bin/linux/ubuntu/README.html
The following packages are required in order for the R scripts, which are used in the pipelines, to run properly:
- [```png```](https://cran.r-project.org/web/packages/png/index.html)
- [```readr```](https://cran.r-project.org/web/packages/png/index.html)
- [```tidyr```](https://cran.r-project.org/web/packages/tidyr/index.html)
- [```dplyr```](https://cran.r-project.org/web/packages/dplyr/index.html)
- [```tibble```](https://cran.r-project.org/web/packages/tibble/index.html)
- [```stringr```](https://cran.r-project.org/web/packages/stringr/index.html)
- [```qiime2R```](https://rdrr.io/github/jbisanz/qiime2R/)
- [```phyloseq```](https://bioconductor.org/packages/release/bioc/html/phyloseq.html)
- [```metacoder```](https://cran.r-project.org/web/packages/metacoder/index.html)
- [```cluster```](https://cran.r-project.org/web/packages/cluster/index.html)
## Documentation
For the [Common Workflow Language](https://www.commonwl.org/) please find instructions here: https://www.commonwl.org/user_guide/
Directories:
* ```R_scripts``` folder contains all R scripts which can be used from the pipeline created
* ```mapping``` folder contains all [metadata]((https://docs.qiime2.org/2018.11/tutorials/metadata/)) files
* ```workflows``` folder contains all pipelines which have been created
* ```wrappers``` folder contains all wrappers which are used from the workflows
* ```yaml_files``` folder contains all YAML files that are used as input for the pipelines
## Usage
1. Create a new directory and place all ```fastq``` files in it
2. Create a metadata file (see ```mapping/manifest``` for an example)
3. [Import your data](https://docs.qiime2.org/2019.7/tutorials/importing/) as a Qiime2 artifact
4. Create a new [classifier](https://docs.qiime2.org/2018.11/data-resources/) or use a pre-trained one
5. Give all paths of your files and any other desirable input in ```yaml_files/fastqc_trim_qiime2.yml```
Run the following command:
```
cwl-runner workflows/fastqc_trim_qiime2.cwl yaml_files/fastqc_trim_qiime2.yml
```
## License
This project is licensed under the GNU General Public License v3.0 - see the [LICENSE](LICENSE) file for details