Documentation

Installing

Before moving forward, make sure you have both docker and nextflow installed in your machine.

Check here to for nextflow and docker installation instructions.

# check for docker version
docker -v
Docker version 24.0.2, build cb74dfc

# check for nextflow version
nextflow -v
nextflow version 23.04.2.5870

Then, clone the repository:

git clone [email protected]:rbtoscan/nextflow_docker.git

After cloning, cd into the repository folder and run the install.sh script. It will create the necessary docker images so that they can be used in the script. This might take from 10 to 20 minutes. If you have a docker image with the same R packages contained in the install/dockerfile/r_task4/Dockerfile, you may consider commenting out this docker build in the install.sh script and replacing the container for an appropriate one in the ryvu_nextflow.nf script.

The script will also attempt to copy one external R script to the /usr/local/bin folder. This might not work for all filesystems, so please copy this file to an appropriate /bin folder so that nextflow can find it later.

cd nextflow_docker/
bash install.sh

Before running

• Check if the docker images are ready. Run “docker images ls” and you should see something like that :

$ docker image ls
REPOSITORY                 TAG       IMAGE ID       CREATED        SIZE
r_task4                    latest    349887f4b439   2 hours ago    1.12GB
r-base                     latest    5441619af0c0   2 weeks ago    822MB
staphb/samtools            latest    1f1fe155547d   5 weeks ago    145MB
staphb/bowtie2             latest    9fb017126d39   3 months ago   734MB

• Check if the task4.R script is accessible. Run “which task4.R” and see if file is found with its path.

$ which task4_genExpress.R
/usr/local/bin/task4_genExpress.R  

• Make sure you have a reference genome to be used for task 1. You may use one of your choice but the reproduce the exact same results, please use the release14. Create a directory, download the genome from NCBI, copy it into it and index it using bowtie2 like so:

bowtie2 GCA_000001405.15_GRCh38_genomic.fna GCA_000001405.15_GRCh38_genomic

Keep track of the location of this folder.

Running

To run the tool

./nextflow run ryvu_nextflow.nf --ref_genome <full path to ref_genome index> --input <full path to library.fa>

Example:

./nextflow run ryvu_nextflow.nf --ref_genome /home/storage/files/ref_genome/GCA_000001405.15_GRCh38_genomic --input /home/storage/files/library.fa

You may also edit the ryvu_nextflow.nf script at the top and replace the param.ref_genome and param.input variables for their corresponding paths. If you do that, you may run without any additional parameters:

./nextflow run ryvu_nextflow.nf