diff --git a/workshop/A_create_graph.ipynb b/workshop/A_create_graph.ipynb index d1be4f9d7a8f2fe20a06f1742adcd4fbd38aa898..0827780b121d81b13e2c721cc639e1ad712b2ca9 100644 --- a/workshop/A_create_graph.ipynb +++ b/workshop/A_create_graph.ipynb @@ -1727,7 +1727,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "## Create slurm script" + "Create slurm script" ] }, { @@ -1742,6 +1742,7 @@ "source": [ "%%bash\n", "\n", + "\n", "echo '\\\n", "#!/bin/bash\n", "\n", @@ -1754,19 +1755,19 @@ "\n", "singularity exec /scicore/home/gagneux/GROUP/PacbioSnake_resources/containers/pggb_latest.sif pggb \\\n", " -i assemblies_combined.fasta.gz \\\n", - " -o ./pggb \\\n", + " -o ./pggb_L1 \\\n", " -m \\\n", " -t 20 \\\n", - " -n 52 \\\n", + " -n 18 \\\n", " -p 99 \\\n", - " -s 5k\n" + " -s 5k' > run_pggb.slrm" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "# Variant calling" + "Submit it" ] }, { @@ -1781,16 +1782,24 @@ "source": [ "%%bash\n", "\n", - "REF=\n", - "\n", - "/scicore/home/gagneux/GROUP/PacbioSnake_resources/containers/pggb_latest.sif vg deconstruct" + "sbatch run_pggb.slrm" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "# Visualization" + "# Visualization\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "https://www.evomicslab.org/app/vrpg/" ] } ], diff --git a/workshop/pics/is6110_ppe.small.png b/workshop/pics/is6110_ppe.small.png new file mode 100644 index 0000000000000000000000000000000000000000..62833af2901e32e5c1ad64b14fe0871998ecdf27 Binary files /dev/null and b/workshop/pics/is6110_ppe.small.png differ