Add SLURM job example for Verkko (#68)

* Add SLURM job example for Verkko * Update verkko_slurm.submit --------- Co-authored-by: Natasha Pavlovikj <[email protected]>
unlhcc · May 8, 2024 · 446ccdb · 446ccdb
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diff --git a/verkko/README.md b/verkko/README.md
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+# Using Verkko on HCC Clusters
+
+Example job script for [Verkko](https://github.com/marbl/verkko), adapted from [here](https://github.com/marbl/verkko?tab=readme-ov-file#test-data).
+
+- `verkko_local.submit`: Example submit script using 4 cores and running on one compute node.
+
+- `verkko_slurm.submit`: Example submit script using 4 cores and submitting multiple jobs to the cluster via [Slurm](https://github.com/marbl/verkko?tab=readme-ov-file#running-on-a-grid).
diff --git a/verkko/verkko_local.submit b/verkko/verkko_local.submit
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+#!/bin/bash
+#SBATCH --job-name=verkko
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=4
+#SBATCH --mem=10G
+#SBATCH --time=01:00:00
+#SBATCH --partition=batch
+#SBATCH --error=verkko.%J.err
+#SBATCH --output=verkko.%J.out
+
+module purge
+module load verkko/2.0
+
+# test data is available at https://github.com/marbl/verkko?tab=readme-ov-file#test-data
+verkko -d asm --hifi ./hifi.fastq.gz --nano ./ont.fastq.gz --threads $SLURM_NTASKS_PER_NODE
diff --git a/verkko/verkko_slurm.submit b/verkko/verkko_slurm.submit
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+#!/bin/bash
+#SBATCH --job-name=verkko
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=4
+#SBATCH --mem=10G
+#SBATCH --time=10:00:00
+#SBATCH --partition=batch
+#SBATCH --error=verkko.%J.err
+#SBATCH --output=verkko.%J.out
+
+module purge
+module load verkko/2.0
+
+# test data is available at https://github.com/marbl/verkko?tab=readme-ov-file#test-data
+verkko -d asm --hifi ./hifi.fastq.gz --nano ./ont.fastq.gz --threads $SLURM_NTASKS_PER_NODE --slurm