From 0f9772f48551c21886f6983c0d7441bd6f0582be Mon Sep 17 00:00:00 2001
From: Jalil Nourisa <jalil.nourisa@gmail.com>
Date: Thu, 19 Sep 2024 16:38:07 +0200
Subject: [PATCH] baseline models are structured. util added:attemp6

---
 runs.ipynb                          | 7 ++++---
 scripts/run_benchmark_all.sh        | 4 ++--
 src/workflows/run_benchmark/main.nf | 1 -
 3 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/runs.ipynb b/runs.ipynb
index d05c554c6..56eca8ce8 100644
--- a/runs.ipynb
+++ b/runs.ipynb
@@ -162,7 +162,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Baseline scores on donor 0. Normalized, non cell type specific, full "
+    "### Baseline scores on donor 0. Normalized, non cell type specific"
    ]
   },
   {
@@ -254,15 +254,16 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Baseline scores on donor 0. non normalized, non cell type specific"
+    "### Baseline scores on donor 0. Not normalized, non cell type specific"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 8,
    "metadata": {},
    "outputs": [],
    "source": [
+    "RUN_ID=\"benchmark_donor_0_baselines_nonspecific_notnormalized\"\n",
     "\n"
    ]
   },
diff --git a/scripts/run_benchmark_all.sh b/scripts/run_benchmark_all.sh
index 2e9a6febe..811bb7c6b 100644
--- a/scripts/run_benchmark_all.sh
+++ b/scripts/run_benchmark_all.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 
 # RUN_ID="run_$(date +%Y-%m-%d_%H-%M-%S)"
-RUN_ID="benchmark_donor_0_baselines_specific"
+RUN_ID="benchmark_donor_0_baselines_nonspecific_notnormalized"
 # resources_dir="./resources_test/"
 resources_dir="s3://openproblems-data/resources/grn"
 publish_dir="${resources_dir}/results/${RUN_ID}"
@@ -11,7 +11,7 @@ subsample=-2
 max_workers=10
 layer='scgen_pearson'
 metric_ids="[regression_1, regression_2]"
-cell_type_specific=true #for controls
+cell_type_specific=false #for controls
 normalize=false
 only_hvgs=false
 # method_ids="[tigress, ennet, scsgl, pidc]"
diff --git a/src/workflows/run_benchmark/main.nf b/src/workflows/run_benchmark/main.nf
index d3a54008f..31e03c8ab 100644
--- a/src/workflows/run_benchmark/main.nf
+++ b/src/workflows/run_benchmark/main.nf
@@ -14,7 +14,6 @@ workflow run_wf {
   // construct list of methods
   methods = [
     portia,
-    ennet,
     genie3,
     grnboost2,
     ppcor,