Github Syncing

One of the coolest things about nextflow is that you can deploy scripts directly from Github - provided the repository is set up correctly.

Go to your local clone of your rtp_workshop repository:

1. Rename test.nf as main.nf.

2. Update your nextflow.config file:

   process{
     container = 'barryd237/test:dev'
     containerOptions = '-B /data/'
   }
   
   params{
     input = "/data/test/test-dataset/fastq/*_{1,2}.fastq.gz"
   }
   
   singularity.enabled = true
   singularity.autoMounts = true
   singularity.cacheDir = '/data/containers'
   

Push the changes to Github:

git add .
git commit -m "Prepare repo for deployment"
git push

The repository can now be deployed directly from GitHub:

nextflow pull BarryDigby/rtp_workshop

nextflow run -r dev BarryDigby/rtp_workshop

Pretty nifty.