@@ -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.
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@@ -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.
