Added progress flag to 06

Author: joannmudge

module_notebooks/06-read-mapping-with-vg.ipynb

@@ -240,11 +240,11 @@
     "<details>\n",
     "<summary>Click for help</summary>\n",
     "<br>\n",
-    "!vg giraffe -Z graphs/yprp.fullgenome.pggb.giraffe.gbz -m graphs/yprp.fullgenome.pggb.min -d graphs/yprp.fullgenome.pggb.dist -f reads/SK1.illumina_1.fastq.gz -f reads/SK1.illumina_2.fastq.gz > alignments/SK1xyprp.fullgenome.pggb.mapped.gam  \n",
+    "!vg giraffe -p -Z graphs/yprp.fullgenome.pggb.giraffe.gbz -m graphs/yprp.fullgenome.pggb.min -d graphs/yprp.fullgenome.pggb.dist -f reads/SK1.illumina_1.fastq.gz -f reads/SK1.illumina_2.fastq.gz > alignments/SK1xyprp.fullgenome.pggb.mapped.gam  \n",
     "\n",
     "<br><br>\n",
     "\n",
-    "!vg giraffe -Z graphs/yprp.allchrs.pggb.giraffe.gbz -m graphs/yprp.allchrs.pggb.min -d graphs/yprp.allchrs.pggb.dist -f reads/SK1.illumina_1.fastq.gz -f reads/SK1.illumina_2.fastq.gz > alignments/SK1xyprp.allchrs.pggb.mapped.gam\n",
+    "!vg giraffe -p -Z graphs/yprp.allchrs.pggb.giraffe.gbz -m graphs/yprp.allchrs.pggb.min -d graphs/yprp.allchrs.pggb.dist -f reads/SK1.illumina_1.fastq.gz -f reads/SK1.illumina_2.fastq.gz > alignments/SK1xyprp.allchrs.pggb.mapped.gam\n",
     "</details>"
    ]
   },
@@ -511,6 +511,12 @@
   }
  ],
  "metadata": {
+  "environment": {
+   "kernel": "conda-env-nigms-pangenomics-nigms-pangenomics",
+   "name": "workbench-notebooks.m127",
+   "type": "gcloud",
+   "uri": "us-docker.pkg.dev/deeplearning-platform-release/gcr.io/workbench-notebooks:m127"
+  },
   "kernelspec": {
    "display_name": "nigms-pangenomics",
    "language": "python",