From 7449f56c4e544b35de0f6b2d9d55dbef9ed29e5b Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 6 Jun 2018 09:20:27 +0200
Subject: [PATCH] TP.md: add cutadapt.config section

---
 doc/TP_experimental_biologists.md | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/doc/TP_experimental_biologists.md b/doc/TP_experimental_biologists.md
index 9ee758b..332f40d 100644
--- a/doc/TP_experimental_biologists.md
+++ b/doc/TP_experimental_biologists.md
@@ -246,6 +246,13 @@ For this  practical, we are going to need the following tools :
 
 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.
 
+If you are using a CBP computer don't forget to cleanup your docker containers at the end of the practical with the following command:
+
+```sh
+docker rm $(docker stop $(docker ps -aq))
+docker rmi $(docker images -qf "dangling=true")
+```
+
 ## Cutadapt
 
 The first step of the pipeline is to remove any Illumina adaptor left in your reads files.
@@ -277,6 +284,19 @@ Channel
 
 As we are working with paired-end RNASeq data we tell nextflow to send pairs of fastq in the `fastq_file` channel.
 
+
+### cutadapt.config
+
+For the `fastq_sampler.nf` pipeline we used the command `head` present in most base UNIX systems. Here we want to use `cutadapt` which is not. Therefore, we have three main options:
+
+- install cutadapt locally so nextflow can use it
+- launch the process in a Docker container that have cutadapt installed
+- launch the process with SGE while loading the correct module to have cutadapt available
+
+We are not going to use the first option which requiere no configuration for nextflow but tedious tools installation. Instead, we are going to use existing *wrappers* and tell nextflow about it. This is what the `src/cutadapt/cutadapt.config` is used for.
+
+Copy the content of this config file to an `src/RNASeq.config` file. This file is structured in process blocks. Here we are only interested in configuring `adaptor_removal` process not `trimming` process. So you can remove the `trimming` block and commit.
+
 You can test your pipeline.
 
 ## UrQt
-- 
GitLab