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cumc · Aug 17, 2023 · f30ad7f · f30ad7f
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diff --git a/README.html b/README.html
@@ -715,7 +715,7 @@ <h3>Organization of the resource<a class="headerlink" href="#organization-of-the
 <div class="section" id="computing-environment-setup">
 <h3>Computing environment setup<a class="headerlink" href="#computing-environment-setup" title="Permalink to this headline">¶</a></h3>
 <ul class="simple">
-<li><p>In order to run the xQTL protocol on your computer (or a High Performance Computing cluster), please install Script of Scripts <a class="reference external" href="https://wanggroup.org/orientation/jupyter-setup">(see here for a tutorial to set it up with <code class="docutils literal notranslate"><span class="pre">micromamba</span></code>)</a>.</p>
+<li><p>In order to run the xQTL protocol on your computer (or a High Performance Computing cluster), please install Script of Scripts (<strong>version &gt; 0.24.1</strong>) <a class="reference external" href="https://wanggroup.org/orientation/jupyter-setup">(see here for a tutorial to set it up with <code class="docutils literal notranslate"><span class="pre">micromamba</span></code>)</a>.</p>
 <ul>
 <li><p>For Linux and Mac desktop users you can either install the container <a class="reference external" href="https://docs.sylabs.io/guides/3.2/user-guide/installation.html"><code class="docutils literal notranslate"><span class="pre">Singularity</span></code></a> or <a class="reference external" href="https://www.docker.com/"><code class="docutils literal notranslate"><span class="pre">Docker</span></code></a>. In the xQTL project we primarily use <code class="docutils literal notranslate"><span class="pre">Singularity</span></code>.</p></li>
 <li><p>For Linux-based HPC users, your system may already have <code class="docutils literal notranslate"><span class="pre">Singularity</span></code> installed. If not please communicate with the IT support for the HPC. Typically Docker is not allowed on HPC.</p></li>

diff --git a/_sources/README.md b/_sources/README.md
@@ -39,7 +39,7 @@ The website https://cumc.github.io/xqtl-pipeline is generated from files under t
 
 ### Computing environment setup
 
-- In order to run the xQTL protocol on your computer (or a High Performance Computing cluster), please install Script of Scripts [(see here for a tutorial to set it up with `micromamba`)](https://wanggroup.org/orientation/jupyter-setup). 
+- In order to run the xQTL protocol on your computer (or a High Performance Computing cluster), please install Script of Scripts (**version > 0.24.1**) [(see here for a tutorial to set it up with `micromamba`)](https://wanggroup.org/orientation/jupyter-setup). 
     - For Linux and Mac desktop users you can either install the container [`Singularity`](https://docs.sylabs.io/guides/3.2/user-guide/installation.html#) or [`Docker`](https://www.docker.com/). In the xQTL project we primarily use `Singularity`.
     - For Linux-based HPC users, your system may already have `Singularity` installed. If not please communicate with the IT support for the HPC. Typically Docker is not allowed on HPC.
     - For Windows users, you will need to install [WSL](https://learn.microsoft.com/en-us/windows/wsl/install) (we have tested it on WSL2 and not on WSL1) and then install `Singularity` within WSL as instructed in this [post](https://www.blopig.com/blog/2021/09/using-singularity-on-windows-with-wsl2/).

diff --git a/_sources/code/data_preprocessing/genotype/VCF_QC.ipynb b/_sources/code/data_preprocessing/genotype/VCF_QC.ipynb
@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "acquired-queen",
+   "id": "noted-verse",
    "metadata": {
     "kernel": "SoS",
     "tags": []
@@ -13,7 +13,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "authentic-railway",
+   "id": "reported-modeling",
    "metadata": {
     "kernel": "SoS"
    },
@@ -23,7 +23,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "peripheral-zimbabwe",
+   "id": "engaging-brisbane",
    "metadata": {
     "kernel": "SoS"
    },
@@ -46,7 +46,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "competent-antarctica",
+   "id": "empirical-intention",
    "metadata": {
     "kernel": "SoS"
    },
@@ -69,7 +69,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "perceived-chicken",
+   "id": "limited-induction",
    "metadata": {
     "kernel": "SoS",
     "tags": []
@@ -94,7 +94,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "entertaining-christmas",
+   "id": "acting-tuning",
    "metadata": {
     "kernel": "SoS"
    },
@@ -112,7 +112,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "coral-genealogy",
+   "id": "rotary-dodge",
    "metadata": {
     "kernel": "SoS"
    },
@@ -134,7 +134,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "comparative-welcome",
+   "id": "ranking-schedule",
    "metadata": {
     "kernel": "SoS"
    },
@@ -177,7 +177,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "foreign-intermediate",
+   "id": "young-negative",
    "metadata": {
     "kernel": "SoS"
    },
@@ -192,7 +192,7 @@
   {
    "cell_type": "code",
    "execution_count": 13,
-   "id": "local-lending",
+   "id": "present-potential",
    "metadata": {
     "kernel": "SoS"
    },
@@ -211,7 +211,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "infinite-estonia",
+   "id": "attempted-protein",
    "metadata": {
     "kernel": "SoS"
    },
@@ -222,7 +222,7 @@
   {
    "cell_type": "code",
    "execution_count": 4,
-   "id": "surrounded-tyler",
+   "id": "aggressive-necessity",
    "metadata": {
     "kernel": "SoS"
    },
@@ -241,7 +241,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "liked-radar",
+   "id": "documentary-importance",
    "metadata": {
     "kernel": "SoS"
    },
@@ -252,7 +252,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "broad-satin",
+   "id": "contemporary-spyware",
    "metadata": {
     "kernel": "SoS"
    },
@@ -264,7 +264,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "occasional-firewall",
+   "id": "certified-strap",
    "metadata": {
     "kernel": "SoS"
    },
@@ -275,7 +275,7 @@
   {
    "cell_type": "code",
    "execution_count": 1,
-   "id": "banner-simon",
+   "id": "sitting-princess",
    "metadata": {
     "kernel": "Bash",
     "tags": []
@@ -374,7 +374,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "altered-fountain",
+   "id": "dutch-advocate",
    "metadata": {
     "kernel": "Bash"
    },
@@ -385,7 +385,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "recent-score",
+   "id": "interstate-building",
    "metadata": {
     "kernel": "SoS"
    },
@@ -469,7 +469,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "dynamic-halloween",
+   "id": "alpha-enhancement",
    "metadata": {
     "kernel": "SoS",
     "tags": []
@@ -485,7 +485,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "sharp-peninsula",
+   "id": "wound-physiology",
    "metadata": {
     "kernel": "SoS"
    },
@@ -506,7 +506,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "stylish-trust",
+   "id": "progressive-vacuum",
    "metadata": {
     "kernel": "SoS"
    },
@@ -537,7 +537,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "stuck-orleans",
+   "id": "representative-college",
    "metadata": {
     "kernel": "SoS"
    },
@@ -550,7 +550,7 @@
   {
    "cell_type": "code",
    "execution_count": 4,
-   "id": "reported-reaction",
+   "id": "baking-liberal",
    "metadata": {
     "kernel": "SoS"
    },
@@ -598,7 +598,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "answering-brooklyn",
+   "id": "hidden-superior",
    "metadata": {
     "kernel": "SoS"
    },
@@ -609,7 +609,7 @@
   {
    "cell_type": "code",
    "execution_count": 3,
-   "id": "affiliated-anchor",
+   "id": "textile-keyboard",
    "metadata": {
     "kernel": "SoS"
    },
@@ -675,14 +675,13 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "little-planet",
+   "id": "fluid-legislature",
    "metadata": {
     "kernel": "SoS"
    },
    "outputs": [],
    "source": [
     "[qc_3 (genotype data summary statistics)]\n",
-    "parameter: walltime = '24h'\n",
     "input: output_from('qc_1'), output_from('qc_2'), group_by = 1\n",
     "output: f\"{cwd}/{_input:bnn}.novel_variant_sumstats\", \n",
     "        f\"{cwd}/{_input:bnn}.known_variant_sumstats\", \n",