Create Job Definition

Create Job-Definition

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Basic Configuration

Now that we have everything, we need to create a job definition. For that click [1].

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  • [1] define the job name: nf-head
  • [2] how often it is able to run before failing: 1
  • [3] the execution timeout (here 1 hour or 3600 seconds): 3600
  • [4] the container image from the docker push before: copy paste the docker url visible in the log after executing the code docker build -t $REPO_URI:${IMG_TAG} . at previous step
  • [5] the entrypoint command: /usr/local/bin/entrypoint.sh
  • [6] and finally how many resources the image needs to run: 1 cpu, 256 Mb memory

Security and Environment

  • Security user: root
    Since the Nextflow config is placed in the $HOME directory of root, we run the process within the container as root ([1]).
  • Environment variables Finally we define environment variables to control which pipeline to run ([2]) and create the job definition ([3]).

Please set 2 environment variables:

  • Key: PIPELINE_URL and value: https://github.com/seqeralabs/nextflow-tutorial.git
  • Key: BUCKET_NAME_RESULTS and value of the environment variable BUCKET_NAME_RESULTS: nextflow-workshop-XXXYYZZZ
  • Key: NF_SCRIPT and value script7.nf.

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