@@ -72,30 +72,58 @@ ls -l src/docker_modules/Bowtie2/2.3.4.1/
-rwxr-xr-x 1 laurent _lpoperator 79 Jun 5 16:18 docker_init.sh*
```
The `Dockerfile` is the [Docker](https://www.docker.com/what-docker) recepi to create a [container](https://www.docker.com/what-container) containing `Bowtie2` in it's `2.3.4.1` version. And the `docker_init.sh` file is a small script to create the [container](https://www.docker.com/what-container) from this recipe.
The `Dockerfile` is the [Docker](https://www.docker.com/what-docker) recipe to create a [container](https://www.docker.com/what-container) containing `Bowtie2` in it's `2.3.4.1` version. And the `docker_init.sh` file is a small script to create the [container](https://www.docker.com/what-container) from this recipe.
By running this script you will be able to easily install tools in different version on your personnal computer and use it in your pipeline. Some of the advantages are:
By running this script you will be able to easily install tools in different version on your personal computer and use it in your pipeline. Some of the advantages are:
- Whatever the computer, the installation and the results will be the same
- You can keep [container](https://www.docker.com/what-container) for old version of tools and run it on new systems (science = reproducibility)
- You don't have to bother with detious installation procedure, somebody else already did the job and wrote a `Dockerfile`.
- You can easly keep [container](https://www.docker.com/what-container) for differents version of the sam tools.
- You don't have to bother with tedious installation procedure, somebody else already did the job and wrote a `Dockerfile`.
- You can easily keep [container](https://www.docker.com/what-container) for different version of the same tools.
### `sge_modules`
The `src/sge_modules` folder is not realy there. It's a submodule of the project [PSMN/modules](https://gitlab.biologie.ens-lyon.fr/PSMN/modules). To populate it locally you can use the following command:
The `src/sge_modules` folder is not really there. It's a submodule of the project [PSMN/modules](https://gitlab.biologie.ens-lyon.fr/PSMN/modules). To populate it locally you can use the following command:
```sh
git submodule init
```
Like for the `src/docker_modules` the [PSMN/modules](https://gitlab.biologie.ens-lyon.fr/PSMN/modules) project describe recepies to install tools and use them. The main difference is that you cannot use [Docker](https://www.docker.com/what-docker) on the PSMN. Instead you have to use another framework [Environement Module](http://www.ens-lyon.fr/PSMN/doku.php?id=documentation:tools:modules) which allows you to load modules for specific tools and version.
Like for the `src/docker_modules` the [PSMN/modules](https://gitlab.biologie.ens-lyon.fr/PSMN/modules) project describe recipes to install tools and use them. The main difference is that you cannot use [Docker](https://www.docker.com/what-docker) on the PSMN. Instead you have to use another framework [Environment Module](http://www.ens-lyon.fr/PSMN/doku.php?id=documentation:tools:modules) which allows you to load modules for specific tools and version.
The [README.md](https://gitlab.biologie.ens-lyon.fr/PSMN/modules/blob/master/README.md) file of the [PSMN/modules](https://gitlab.biologie.ens-lyon.fr/PSMN/modules) respository contains all the instruction to be able to load the modules maintained by the LBMC en present in the [PSMN/modules](https://gitlab.biologie.ens-lyon.fr/PSMN/modules) respository.
### `nf_modules`
The `src/nf_modules` folder contains templates of [nextflow](https://www.nextflow.io/) wrapper for the tools available in [Docker](https://www.docker.com/what-docker) and [SGE](http://www.ens-lyon.fr/PSMN/doku.php?id=documentation:tools:sge). The details of the [nextflow](https://www.nextflow.io/) wrapper will be presented in the next section. Alongside the `.nf` and `.config` there is a `tests` folder that contains a `tests.sh` script to run test on the tool.
# Build your own RNASeq pipeline
In this section you are going to build your own pipeline for RNASeq analysis from the code available in the `src/nf_modules` folder.
## Nextflow pipeline
A pipeline is a succession of **process**. Each process has data input(s) and optional data output(s). Data flow are modeled as **channels**.
For this practical, we are going to need the following tools :
- For Illumina adaptor removal : cutadapt
- For reads trimming by quality : UrQt
- For mapping and quantifying reads : Kallisto, RSEM and Bowtie2
To initialize these tools, follow the **Installing** section of the [README.md](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/README.md) file.
