From 8f2097a6728e7027e82517cbd9535713d0353c1c Mon Sep 17 00:00:00 2001 From: Laurent Modolo <laurent.modolo@ens-lyon.fr> Date: Tue, 5 Jun 2018 15:03:28 +0200 Subject: [PATCH] TP_experimental_biologists.md: add cmd for pdf --- doc/TP_experimental_biologists.md | 25 +++++++++++++++++++++++-- 1 file changed, 23 insertions(+), 2 deletions(-) diff --git a/doc/TP_experimental_biologists.md b/doc/TP_experimental_biologists.md index 218b6230..ca1fc3fd 100644 --- a/doc/TP_experimental_biologists.md +++ b/doc/TP_experimental_biologists.md @@ -1,12 +1,33 @@ +--- +title: "TP for experimental biologists" +author: Laurent Modolo [laurent.modolo@ens-lyon.fr](mailto:laurent.modolo@ens-lyon.fr) +date: 6 Jun 2018 +output: + pdf_document: + toc: true + toc_depth: 3 + number_sections: true + highlight: tango + 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. +For this we are going to build a small RNASeq analysis pipeline that should run the following steps: + +- remove Illumina adaptors +- trim reads by quality +- build the index of a reference genome +- estimate the number of RNA fragments mapping to the transcript of this genome ## 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 weel, you can use the [pipelines/nextflow](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow) as a template. +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 means that you are going to make your own private copy of a repository. \ No newline at end of file +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. + + -- GitLab