RNA-Seq toy pipeline

A proof of concept of a RNA-Seq pipeline intended to show Nextflow scripting and reproducibility capabilities.

How execute it using UFRC

1. Login to UFRC

2. Load Singularity

   ml singularity

3. Pull the required Docker image in /home//singularity as shown below:

   singularity pull docker://nextflow/rnatoy:1.3`

4. Upload GitHub repository in /home//rnatoy as shown below:

   curl https://github.com/nextflow-io/rnatoy.git

5. Modify main.nf file: line 33-36 as shown below:

params.reads = "/home//rnatoy/data/ggal/*_{1,2}.fq" params.annot = "/home//rnatoy/data/ggal/ggal_1_48850000_49020000.bed.gff" params.genome = "/home//rnatoy/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa" params.outdir = 'results'

6. Change directory to /home//rnatoy as shown below:

cd /home//rnatoy

7. Run the nextflow script inside the singularity image as shown below:

nextflow run main.nf -with-singularity /home/djlemas/singularity/rnatoy-1.3.simg