From 7359e07ae97590940cc3ec384ef253ea0e4541d3 Mon Sep 17 00:00:00 2001 From: plample Date: Wed, 22 Apr 2020 16:56:32 +0200 Subject: [PATCH] Suggestions to guide and allow copy/paste of value --- .../40_nextflow202/35_batch-squared-run.md | 21 +++++++++++-------- 1 file changed, 12 insertions(+), 9 deletions(-) diff --git a/content/nextflow-on-aws-batch/40_nextflow202/35_batch-squared-run.md b/content/nextflow-on-aws-batch/40_nextflow202/35_batch-squared-run.md index fa1624b3..0628ddaa 100644 --- a/content/nextflow-on-aws-batch/40_nextflow202/35_batch-squared-run.md +++ b/content/nextflow-on-aws-batch/40_nextflow202/35_batch-squared-run.md @@ -14,19 +14,22 @@ Now that we have everything, we need to create a job definition. For that click ![](/images/nextflow-on-aws-batch/nextflow202/create_jobdef_1.png) - - **[1]** define the job name - - **[2]** how often it is able to run before failing - - **[3]** the execution timeout (here 1h) - - **[4]** the container image from the docker push before - - **[5]** the entrypoint command - - **[6]** and finally how many resources the image needs to run. + - **[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]**. +- **Environement variables** Finally we define environment variables to control which pipeline to run **[2]** and create the job definition. -Please set `PIPELINE_URL` to `https://github.com/seqeralabs/nextflow-tutorial.git` and `NF_SCRIPT` to `script7.nf`. +Please set 2 environement variables: +- Key: `PIPELINE_URL` and Value: `https://github.com/seqeralabs/nextflow-tutorial.git` +- Key: `NF_SCRIPT` and Value `script7.nf`. -![](/images/nextflow-on-aws-batch/nextflow202/create_jobdef_2.png) \ No newline at end of file +![](/images/nextflow-on-aws-batch/nextflow202/create_jobdef_2.png)