diff --git a/doc/TP_experimental_biologists.md b/doc/TP_experimental_biologists.md index ca1fc3fd596d5a5500ed3e3fd1de17ec8cb269a6..ec5d07f845e397a89f33ba2a75957e956e1ff2c9 100644 --- a/doc/TP_experimental_biologists.md +++ b/doc/TP_experimental_biologists.md @@ -11,9 +11,7 @@ output: latex_engine: xelatex --- -# TP for experimental biologists - -The Goal of this practical is to learn how to build your own pipeline with nextflow and using the tools already *wrapped* in Docker and SGE. +The Goal of this practical is to learn how to build your own pipeline with nextflow and using the tools already *wrapped*. For this we are going to build a small RNASeq analysis pipeline that should run the following steps: - remove Illumina adaptors @@ -21,13 +19,17 @@ For this we are going to build a small RNASeq analysis pipeline that should run - build the index of a reference genome - estimate the number of RNA fragments mapping to the transcript of this genome -## Initialize your own project +# Initialize your own project You are going to build a pipeline for you or your team. So the first step is to create your own project. Instead of reinventing the wheel, you can use the [pipelines/nextflow](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow) as a template. To easily do so, go to the [pipelines/nextflow](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow) repository and click on the [**fork**](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/forks/new) button. + + In git, the [action of forking](https://git-scm.com/book/en/v2/GitHub-Contributing-to-a-Project) means that you are going to make your own private copy of a repository. You can then write modifications in your project, and if they are of interest for the source repository (here [pipelines/nextflow](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow)) create a merge request. Merge request are send to the source repository to ask the maintainers to integrate modifications. + +