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Fix sbatch submission lab2
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content/04-container-parallelcluster/04-launch-nextflow.md

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@@ -67,6 +67,8 @@ They can be made available inside the running container by binding the external
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In the case of running Nextflow for this lab, the `/shared/nextflow-tutorial` directory contains the workflow description in `scripts7.nf` that will be executed by Nextflow.
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One the job will complete, results will be stored in the `--outdir=/mnt` of the container that is the `/shared/nextflow-tutorial` directory of the cluster where the results will be stored.
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Let's create a slurm batch script with the following command:
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```bash
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cat > nextflow_sub.sh << EOF
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#!/bin/bash
@@ -81,7 +83,13 @@ srun singularity run --bind /shared/nextflow-tutorial:/mnt docker://`echo ${CONT
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EOF
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```
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The output will be similar to this:
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Submit the job to Slurm to run on 1 c5.xlarge instance the nextflow genomics pipeline composed of 4 steps with the following command:
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```bash
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sbatch nextflow_sub.sh
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```
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The output of the job will be in the `nextflow_[SLURM_JOB_ID].out` file and similar to this:
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![Singularity run](/images/container-pc/singularity_nextflow.png)
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