diff --git a/doc/TP_experimental_biologists.md b/doc/TP_experimental_biologists.md index 9ee758bcb6ef9470d1cb5c9d2af62a373af83281..332f40d8c6adad2181306c1965f6149319b78c0a 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