From 4ad3cfc4963f3c6b6fd2a0ff27aa966d35a0e73c Mon Sep 17 00:00:00 2001 From: Carlos Gomes Date: Thu, 10 Jul 2025 17:40:18 -0300 Subject: [PATCH] up: add slurm script example to doc --- README.md | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) diff --git a/README.md b/README.md index 5219af8..8e460b4 100755 --- a/README.md +++ b/README.md @@ -321,6 +321,39 @@ Alternatively, you can make use of an existing [configuration profile](#config- nextflow ./src/main.nf -profile human_blood_basecall ``` +### Slurm script + +The pipeline can be executed in an HPC environment using [Slurm](https://slurm.schedmd.com/). A job submission template for basecalling with the `human_blood_basecall` profile is provided below. + +1. Create a shell script: + + ```sh + nano hb_basecall.sh + ``` + +1. Add and edit the following template: + + ```sh + #!/bin/sh + #SBATCH --time 1-0 + #SBATCH --error basecall_err.log + #SBATCH --output basecall_out.log + #SBATCH --mem 24G + #SBATCH --cpus-per-task 12 + #SBATCH --gpus 3 + srun nextflow run ./src/main.nf \ + -profile human_blood_basecall \ + --basecall_mods "5mC_5hmC,6mA" + ``` + +1. Make the file executable and submit the job to the queue: + + ```sh + chmod +x hb_basecall.sh + sbatch hb_basecall.sh + squeue + ``` + [top](#table-of-contents) ## Useful links -- GitLab