Create Job Definition
Create Job-Definition

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

- [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
.
