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:
1cpu,256Mb memory
Security and Environment
- Security user:
root
Since the Nextflow config is placed in the$HOMEdirectory of root, we run the process within the container asroot([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_URLand value:https://github.com/seqeralabs/nextflow-tutorial.git - Key:
BUCKET_NAME_RESULTSand value of the environment variableBUCKET_NAME_RESULTS:nextflow-workshop-XXXYYZZZ - Key:
NF_SCRIPTand valuescript7.nf.
