Merge pull request #106 from opain/dev

Dev
opain · Jun 13, 2024 · cf47843 · cf47843
2 parents 7d24d31 + 5f3a79b
commit cf47843
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diff --git a/.github/workflows/build_deploy_container.yaml b/.github/workflows/build_deploy_container.yaml
@@ -4,6 +4,10 @@ on:
   release:
     types: [created]
   workflow_dispatch:
+      inputs:
+        tag:
+          description: 'Tag for the release'
+          required: true
 
 jobs:
   build-and-deploy:
@@ -16,7 +20,8 @@ jobs:
       DOCKER_IMAGE_NAME: opaino/genopred_pipeline
       SINGULARITY_IMAGE_NAME: library://opain/genopred
       IMAGE_TAG: ${{ github.ref_name }}
-
+      DOCKERFILE_PATH: pipeline/misc/docker/Dockerfile
+
     steps:
     - name: Checkout code
       uses: actions/checkout@v2
@@ -29,7 +34,7 @@ jobs:
 
     - name: Build and Push Docker Image
       run: |
-        docker buildx build --platform linux/amd64 -t $DOCKER_IMAGE_NAME:latest -t $DOCKER_IMAGE_NAME:$IMAGE_TAG --push .
+        docker buildx build --platform linux/amd64 -f $DOCKERFILE_PATH -t $DOCKER_IMAGE_NAME:latest -t $DOCKER_IMAGE_NAME:${{ github.event.inputs.tag }} --push .
 
     - name: Install Singularity
       run: |
@@ -47,5 +52,6 @@ jobs:
     - name: Push Singularity Image to Singularity Library
       run: |
         singularity push ${GITHUB_WORKSPACE}/image.sif $SINGULARITY_IMAGE_NAME:latest
-        singularity build ${GITHUB_WORKSPACE}/image_$IMAGE_TAG.sif docker-daemon://${DOCKER_IMAGE_NAME}:$IMAGE_TAG
-        singularity push ${GITHUB_WORKSPACE}/image_$IMAGE_TAG.sif $SINGULARITY_IMAGE_NAME:$IMAGE_TAG
+        singularity build ${GITHUB_WORKSPACE}/image_${{ github.event.inputs.tag }}.sif docker-daemon://${DOCKER_IMAGE_NAME}:${{ github.event.inputs.tag }}
+        singularity push ${GITHUB_WORKSPACE}/image_${{ github.event.inputs.tag }}.sif $SINGULARITY_IMAGE_NAME:${{ github.event.inputs.tag }}
+        
diff --git a/docs/pipeline_overview.Rmd b/docs/pipeline_overview.Rmd
@@ -51,8 +51,9 @@ The pipeline uses the Snakemake workflow manager and conda environments providin
 
 ***
 
-**Please cite the following paper** when you use the GenoPred pipeline: 
-Pain, Oliver, et al. "Evaluation of polygenic prediction methodology within a reference-standardized framework." PLoS genetics 17.5 (2021): e1009021.
+# Preprint
+
+Check out our preprint describing the pipeline: "The GenoPred Pipeline: A Comprehensive and Scalable Pipeline for Polygenic Scoring." - <a href="https://doi.org/10.1101/2024.06.12.24308843" class="inline_button">Link</a>
 
 ***
 

diff --git a/docs/pipeline_overview.html b/docs/pipeline_overview.html
@@ -13,7 +13,7 @@
 
 <title>GenoPred Pipeline</title>
 
-<script src="site_libs/header-attrs-2.25/header-attrs.js"></script>
+<script src="site_libs/header-attrs-2.26/header-attrs.js"></script>
 <script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
 <meta name="viewport" content="width=device-width, initial-scale=1" />
 <link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" />
@@ -389,10 +389,13 @@ <h1>Promo Video</h1>
 <iframe width="560" height="315" src="https://www.youtube.com/embed/dKiG8Udz0rI?si=umolv53Scyh1a4fL" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen>
 </iframe>
 <hr />
-<p><strong>Please cite the following paper</strong> when you use the
-GenoPred pipeline: Pain, Oliver, et al. “Evaluation of polygenic
-prediction methodology within a reference-standardized framework.” PLoS
-genetics 17.5 (2021): e1009021.</p>
+</div>
+<div id="preprint" class="section level1">
+<h1>Preprint</h1>
+<p>Check out our preprint describing the pipeline: “The GenoPred
+Pipeline: A Comprehensive and Scalable Pipeline for Polygenic Scoring.”
+-
+<a href="https://doi.org/10.1101/2024.06.12.24308843" class="inline_button">Link</a></p>
 <hr />
 </div>
 <div id="any-questions" class="section level1">

diff --git a/docs/pipeline_readme.Rmd b/docs/pipeline_readme.Rmd
@@ -39,9 +39,13 @@ For a technical details of the GenoPred pipeline, click [here](pipeline_technica
 
 **Citations**
 
-Please cite our paper describing the reference-standardised approach used by the GenoPred pipeline: 
+Please cite our preprint when using the pipeline:
 
-- Pain, Oliver, et al. "Evaluation of polygenic prediction methodology within a reference-standardized framework." PLoS genetics 17.5 (2021): e1009021.
+- "Pain, O. et al. "The GenoPred Pipeline: A Comprehensive and Scalable Pipeline for Polygenic Scoring." MedRxiv 2024. https://doi.org/10.1101/2024.06.12.24308843
+
+If relevant, please also cite our paper comparing polygenic scoring methods and describing the reference-standardised approach:
+
+- Pain, O. et al. "Evaluation of polygenic prediction methodology within a reference-standardized framework." PLoS genetics. https://doi.org/10.1371/journal.pgen.1009021
 
 Please also cite the relevant studies for the tools and data used by the GenoPred pipeline.
 

diff --git a/docs/pipeline_readme.html b/docs/pipeline_readme.html
@@ -449,12 +449,20 @@ <h1 class="title toc-ignore">GenoPred Pipeline - Instructions</h1>
 GenoPred pipeline, click <a href="pipeline_technical.html">here</a>.</p>
 <hr />
 <p><strong>Citations</strong></p>
-<p>Please cite our paper describing the reference-standardised approach
-used by the GenoPred pipeline:</p>
+<p>Please cite our preprint when using the pipeline:</p>
 <ul>
-<li>Pain, Oliver, et al. “Evaluation of polygenic prediction methodology
-within a reference-standardized framework.” PLoS genetics 17.5 (2021):
-e1009021.</li>
+<li>“Pain, O. et al. ”The GenoPred Pipeline: A Comprehensive and
+Scalable Pipeline for Polygenic Scoring.” MedRxiv 2024. <a
+href="https://doi.org/10.1101/2024.06.12.24308843"
+class="uri">https://doi.org/10.1101/2024.06.12.24308843</a></li>
+</ul>
+<p>If relevant, please also cite our paper comparing polygenic scoring
+methods and describing the reference-standardised approach:</p>
+<ul>
+<li>Pain, O. et al. “Evaluation of polygenic prediction methodology
+within a reference-standardized framework.” PLoS genetics. <a
+href="https://doi.org/10.1371/journal.pgen.1009021"
+class="uri">https://doi.org/10.1371/journal.pgen.1009021</a></li>
 </ul>
 <p>Please also cite the relevant studies for the tools and data used by
 the GenoPred pipeline.</p>

diff --git a/docs/pipeline_technical.Rmd b/docs/pipeline_technical.Rmd
@@ -24,8 +24,15 @@ library(data.table)
 
 This document provides technical details of the GenoPred pipeline. The GenoPred pipeline automates the process of calculating polygenic scores. The pipeline aims to implement the current practises for polygenic scoring. See [here](pipeline_overview.html) more general information regarding the GenoPred pipeline.
 
-**Please cite the following paper** when you use the GenoPred pipeline: 
-Pain, Oliver, et al. "Evaluation of polygenic prediction methodology within a reference-standardized framework." PLoS genetics 17.5 (2021): e1009021.
+Please cite our preprint when using the pipeline:
+
+- "Pain, O. et al. "The GenoPred Pipeline: A Comprehensive and Scalable Pipeline for Polygenic Scoring." MedRxiv 2024. https://doi.org/10.1101/2024.06.12.24308843
+
+If relevant, please also cite our paper comparing polygenic scoring methods and describing the reference-standardised approach:
+
+- Pain, O. et al. "Evaluation of polygenic prediction methodology within a reference-standardized framework." PLoS genetics. https://doi.org/10.1371/journal.pgen.1009021
+
+Please also cite the relevant studies for the tools and data used by the GenoPred pipeline.
 
 ***
 

diff --git a/docs/pipeline_technical.html b/docs/pipeline_technical.html
@@ -437,10 +437,23 @@ <h1>Introduction</h1>
 scores. The pipeline aims to implement the current practises for
 polygenic scoring. See <a href="pipeline_overview.html">here</a> more
 general information regarding the GenoPred pipeline.</p>
-<p><strong>Please cite the following paper</strong> when you use the
-GenoPred pipeline: Pain, Oliver, et al. “Evaluation of polygenic
-prediction methodology within a reference-standardized framework.” PLoS
-genetics 17.5 (2021): e1009021.</p>
+<p>Please cite our preprint when using the pipeline:</p>
+<ul>
+<li>“Pain, O. et al. ”The GenoPred Pipeline: A Comprehensive and
+Scalable Pipeline for Polygenic Scoring.” MedRxiv 2024. <a
+href="https://doi.org/10.1101/2024.06.12.24308843"
+class="uri">https://doi.org/10.1101/2024.06.12.24308843</a></li>
+</ul>
+<p>If relevant, please also cite our paper comparing polygenic scoring
+methods and describing the reference-standardised approach:</p>
+<ul>
+<li>Pain, O. et al. “Evaluation of polygenic prediction methodology
+within a reference-standardized framework.” PLoS genetics. <a
+href="https://doi.org/10.1371/journal.pgen.1009021"
+class="uri">https://doi.org/10.1371/journal.pgen.1009021</a></li>
+</ul>
+<p>Please also cite the relevant studies for the tools and data used by
+the GenoPred pipeline.</p>
 <hr />
 </div>
 <div id="software" class="section level1">

diff --git a/pipeline/misc/docker/Dockerfile b/pipeline/misc/docker/Dockerfile
@@ -1,41 +1,41 @@
-# Use the base image
-FROM ubuntu:latest
-
-# Run commands in a single RUN layer to reduce the image size
-RUN apt-get update && \
-    apt-get install -y git curl wget zip gzip vim build-essential zlib1g-dev jq && \
-
-    # Create a wrapper script for tar that includes --no-same-owner
-    echo '#!/bin/sh' > /usr/local/bin/tar && \
-    echo 'exec /bin/tar --no-same-owner "$@"' >> /usr/local/bin/tar && \
-    chmod +x /usr/local/bin/tar
-
-# Install Mambaforge
-RUN wget https://github.com/conda-forge/miniforge/releases/download/4.10.3-10/Mambaforge-4.10.3-10-Linux-x86_64.sh && \
-    bash Mambaforge-4.10.3-10-Linux-x86_64.sh -b -p /opt/mambaforge && \
-    rm Mambaforge-4.10.3-10-Linux-x86_64.sh
-
-# Download GenoPred
-RUN mkdir -p /tools/GenoPred && \
-    cd /tools/GenoPred && \
-    git clone --depth 1 --branch v2.2.7 https://github.com/opain/GenoPred.git . && \
-    git fetch --tags
-
-# Create genopred env
-RUN /opt/mambaforge/bin/conda init bash && \
-    echo "source /opt/mambaforge/etc/profile.d/conda.sh" >> /etc/bash.bashrc && \
-    . /opt/mambaforge/etc/profile.d/conda.sh && \
-    mamba env update -n genopred -f /tools/GenoPred/pipeline/envs/pipeline.yaml && \
-    mamba clean -a -y
-
-# Run initial snakemake command to setup dependencies
-RUN /opt/mambaforge/bin/conda init bash && \
-    echo "source /opt/mambaforge/etc/profile.d/conda.sh" >> /etc/bash.bashrc && \
-    . /opt/mambaforge/etc/profile.d/conda.sh && \
-    conda activate genopred && \
-    cd /tools/GenoPred/pipeline && \
-    snakemake --restart-times 3 -j1 --use-conda --conda-frontend mamba install_r_packages resources/software/pgscatalog_utils/download_pgscatalog_utils.done && \
-    mamba clean -a -y
-
-ENTRYPOINT ["/bin/bash"]
-CMD ["-c", "source /opt/mambaforge/etc/profile.d/conda.sh && conda init && source ~/.bashrc && conda activate genopred && cd /tools/GenoPred/pipeline && exec /bin/bash"]
+# Use the base image
+FROM ubuntu:latest
+
+# Run commands in a single RUN layer to reduce the image size
+RUN apt-get update && \
+    apt-get install -y git curl wget zip gzip vim build-essential zlib1g-dev jq && \
+
+    # Create a wrapper script for tar that includes --no-same-owner
+    echo '#!/bin/sh' > /usr/local/bin/tar && \
+    echo 'exec /bin/tar --no-same-owner "$@"' >> /usr/local/bin/tar && \
+    chmod +x /usr/local/bin/tar
+
+# Install Mambaforge
+RUN wget https://github.com/conda-forge/miniforge/releases/download/4.10.3-10/Mambaforge-4.10.3-10-Linux-x86_64.sh && \
+    bash Mambaforge-4.10.3-10-Linux-x86_64.sh -b -p /opt/mambaforge && \
+    rm Mambaforge-4.10.3-10-Linux-x86_64.sh
+
+# Download GenoPred
+RUN mkdir -p /tools/GenoPred && \
+    cd /tools/GenoPred && \
+    git clone --depth 1 https://github.com/opain/GenoPred.git . && \
+    git fetch --tags
+
+# Create genopred env
+RUN /opt/mambaforge/bin/conda init bash && \
+    echo "source /opt/mambaforge/etc/profile.d/conda.sh" >> /etc/bash.bashrc && \
+    . /opt/mambaforge/etc/profile.d/conda.sh && \
+    mamba env update -n genopred -f /tools/GenoPred/pipeline/envs/pipeline.yaml && \
+    mamba clean -a -y
+
+# Run initial snakemake command to setup dependencies
+RUN /opt/mambaforge/bin/conda init bash && \
+    echo "source /opt/mambaforge/etc/profile.d/conda.sh" >> /etc/bash.bashrc && \
+    . /opt/mambaforge/etc/profile.d/conda.sh && \
+    conda activate genopred && \
+    cd /tools/GenoPred/pipeline && \
+    snakemake --restart-times 3 -j1 --use-conda --conda-frontend mamba install_r_packages resources/software/pgscatalog_utils/download_pgscatalog_utils.done && \
+    mamba clean -a -y
+
+ENTRYPOINT ["/bin/bash"]
+CMD ["-c", "source /opt/mambaforge/etc/profile.d/conda.sh && conda init && source ~/.bashrc && conda activate genopred && cd /tools/GenoPred/pipeline && exec /bin/bash"]