Verified Commit 955c41f2 authored by Laurent Modolo's avatar Laurent Modolo
Browse files

TP.md: add bedtool section

parent b6575e65
......@@ -242,7 +242,7 @@ For this practical, we are going to need the following tools :
- For Illumina adaptor removal : cutadapt
- For reads trimming by quality : UrQt
- For mapping and quantifying reads : Kallisto, Bowtie2
- For mapping and quantifying reads : BEDtools and Kallisto
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.
......@@ -293,11 +293,16 @@ For the `fastq_sampler.nf` pipeline we used the command `head` present in most b
- 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.
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/nf_modules/cutadapt/cutadapt.config](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/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.
You can test your pipeline with the following command:
```sh
./nextflow src/RNASeq.nf -c src/RNASeq.config -profile docker --fastq "data/tiny_dataset/fastq/*_R{1,2}.fastq"
```
## UrQt
......@@ -313,21 +318,31 @@ Therefore, you need to change the line :
set pair_id, file(reads) from fastq_files
```
In the the `trimming` process to:
In the `trimming` process to:
```Groovy
set pair_id, file(reads) from fastq_files_cut
```
The two processes are now connected by the channel `fastq_files_cut`.
Add the content of the [src/nf_modules/UrQt/urqt.config](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/UrQt/urqt.config) file to your `src/RNASeq.config` file and commit.
You can test your pipeline.
## Kallisto
## BEDtools
Kallisto need the sequences of the transcript that need to be quantified. We are going to extract these sequences from the reference `data/tiny_dataset/fasta/tiny_v2.fasta` with the `bed` annotation `data/tiny_dataset/annot/tiny.bed`.
You can copy to your `src/RNASeq.nf` file the content of [src/nf_modules/BEDtools/bedtools.nf](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/BEDtools/bedtools.nf) and to your `src/RNASeq.config` file the content of [src/nf_modules/BEDtools/bedtools.config](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/BEDtools/bedtools.config).
Commit your work and test your pipeline with the following command :
```sh
./nextflow src/RNASeq.nf -c src/RNASeq.config -profile docker --fastq "data/tiny_dataset/fastq/*_R{1,2}.fastq" --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" --bed "data/tiny_dataset/annot/tiny.bed"
```
## Kallisto
......
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