From 6c6c0262a99928dc1a1152a9e9393609f43a2a80 Mon Sep 17 00:00:00 2001
From: Lukas Heumos <lukas.heumos@posteo.net>
Date: Tue, 22 Aug 2023 07:35:02 -0700
Subject: [PATCH] :sparkles: Add nextflow execution ID tracking (#11)

* :sparkles: Add nextflow execution ID tracking

Signed-off-by: zethson <lukas.heumos@posteo.net>

* :bug: Don't resume

Signed-off-by: zethson <lukas.heumos@posteo.net>

* :bug: Use nextflow log

Signed-off-by: zethson <lukas.heumos@posteo.net>

* :sparkles: Simplify

Signed-off-by: zethson <lukas.heumos@posteo.net>

---------

Signed-off-by: zethson <lukas.heumos@posteo.net>
---
 docs/guide/bulk_rna_seq.ipynb | 32 ++++++++++++++++++++++++++++++--
 1 file changed, 30 insertions(+), 2 deletions(-)

diff --git a/docs/guide/bulk_rna_seq.ipynb b/docs/guide/bulk_rna_seq.ipynb
index 1cb95cc..b7ce857 100644
--- a/docs/guide/bulk_rna_seq.ipynb
+++ b/docs/guide/bulk_rna_seq.ipynb
@@ -229,7 +229,7 @@
    },
    "outputs": [],
    "source": [
-    "!nextflow run nf-core/rnaseq -r 3.11.2 -profile test,docker --outdir rna-seq-results -name {ln.dev.run_context.run.id} -resume"
+    "!nextflow run nf-core/rnaseq -r 3.11.2 -profile test,docker --outdir rna-seq-results -name {ln.dev.run_context.run.id}"
    ]
   },
   {
@@ -317,6 +317,34 @@
     "To make the count matrix queryable by biological entities (genes, experimental metadata, etc.), we can now proceed with: {doc}`docs:bulkrna`"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "429bf863",
+   "metadata": {},
+   "source": [
+    "## Register the Nextflow execution id\n",
+    "\n",
+    "If we want to be able to query LaminDB for Nextflow execution ID, this here is a way to get it:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "4c14e053",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import subprocess\n",
+    "\n",
+    "command = f\"nextflow log | grep -F '{ln.dev.run_context.run.id}' | awk '{{print $8}}'\"\n",
+    "session_id = subprocess.getoutput(command)\n",
+    "\n",
+    "run = ln.Run.filter(transform__name=\"nf-core rnaseq\").order_by(\"-run_at\").first()\n",
+    "run.reference = session_id\n",
+    "run.reference_type = \"nextflow_id\"\n",
+    "run.save()"
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "9f607150",
@@ -400,7 +428,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.16"
+   "version": "3.10.12"
   },
   "nbproject": {
    "id": "8124Vtle6ZrO",