Address Nextflow linting, add param validation, reformatting

.github/workflows/build-push-container.yml

@@ -4,7 +4,11 @@ name: build-push-container
 # Configures this workflow to run every time a change is pushed to the branch called `release`.
 on:
   push:
-    branches: ['main']
+    paths:
+      - '**/env.yml'
+      - '**/Dockerfile'
+      - '**/*.dockerfile'
+      - '.github/workflows/build-push-container.yml'
   workflow_dispatch:
 
 # Defines two custom environment variables for the workflow. These are used for the Container registry domain, and a name for the Docker image that this workflow builds.
@@ -39,6 +43,9 @@ jobs:
         uses: docker/metadata-action@9ec57ed1fcdbf14dcef7dfbe97b2010124a938b7
         with:
           images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+          tags: |
+            type=sha,format=short,prefix= # Generates a tag like '860c190'
+            main
       # This step uses the `docker/build-push-action` action to build the image, based on your repository's `Dockerfile`. If the build succeeds, it pushes the image to GitHub Packages.
       # It uses the `context` parameter to define the build's context as the set of files located in the specified path. For more information, see "[Usage](https://github.com/docker/build-push-action#usage)" in the README of the `docker/build-push-action` repository.
       # It uses the `tags` and `labels` parameters to tag and label the image with the output from the "meta" step.

Dockerfile

@@ -1,22 +1,45 @@
-FROM condaforge/miniforge3:24.9.2-0
+FROM mambaorg/micromamba:1.5.8
 
-# Copy the environment file into /tmp
+# Ensure we run as root for apt
+USER root
+
+# Update the conda base environment with required packages
 COPY env.yml /tmp/env.yml
+WORKDIR /tmp
 
-# Install system dependencies
-RUN apt-get update \
-    && apt-get install -y \
-    build-essential \
-    curl \
-    gcc \
-    g++ \
+RUN apt-get update && apt-get install -y \
+        # runtime CLIs (KEEP)
+        curl \
+        wget \
+        git \
+        unzip \
+        zip \
+        jq \
+        procps \
+        \
+        # build-only deps (REMOVE LATER)
+        build-essential \
+        gcc \
+        g++ \
+    && micromamba install -y -n base -f /tmp/env.yml \
+    && micromamba clean -afy \
+    \
+    # R packages (need compilers)
+    && micromamba run -n base Rscript -e "remotes::install_github('HetzDra/turboGliph@2a5264b')" \
+    && micromamba run -n base Rscript -e "remotes::install_github('kalaga27/tcrpheno@56f9372')" \
+    \
+    # R cleanup
+    && rm -rf /tmp/Rtmp* /root/.cache/R \
+    \
+    # REMOVE build deps ONLY
+    && apt-get purge -y \
+        build-essential \
+        gcc \
+        g++ \
+    && apt-get autoremove -y \
     && apt-get clean \
     && rm -rf /var/lib/apt/lists/*
 
-# Update the conda base environment with required packages
-WORKDIR /tmp
-RUN conda env update -n base --file env.yml
-
 # Install GIANA, patch shebang, symlink for PATH command availability
 RUN git init /opt/GIANA && \
     cd /opt/GIANA && \
@@ -29,26 +52,20 @@ RUN git init /opt/GIANA && \
 
 # Install quarto
 RUN mkdir -p /opt/quarto/1.6.42 \
-    && curl -o quarto.tar.gz -L \
+    && curl -o /tmp/quarto.tar.gz -L \
         "https://github.com/quarto-dev/quarto-cli/releases/download/v1.6.42/quarto-1.6.42-linux-amd64.tar.gz" \
-    && tar -zxvf quarto.tar.gz \
+    && tar -zxvf /tmp/quarto.tar.gz \
         -C "/opt/quarto/1.6.42" \
         --strip-components=1 \
-    && rm quarto.tar.gz 
+    && rm /tmp/quarto.tar.gz 
 
-# Install R package not available via conda
-RUN Rscript -e "remotes::install_github('HetzDra/turboGliph')"
-RUN Rscript -e "remotes::install_github('kalaga27/tcrpheno')"
-
-# Install VDJmatch
+# Install VDJmatch and symlink
 RUN mkdir -p /opt/vdjmatch/1.3.1 \
     && curl -L -o vdjmatch.zip \
         "https://github.com/antigenomics/vdjmatch/releases/download/1.3.1/vdjmatch-1.3.1.zip" \
     && unzip vdjmatch.zip -d /opt/vdjmatch/1.3.1 \
-    && rm vdjmatch.zip
-
-# symlink VDJmatch
-RUN ln -s /opt/vdjmatch/1.3.1/vdjmatch-1.3.1/vdjmatch-1.3.1.jar /usr/local/bin/vdjmatch.jar
+    && rm vdjmatch.zip \
+    && ln -s /opt/vdjmatch/1.3.1/vdjmatch-1.3.1/vdjmatch-1.3.1.jar /usr/local/bin/vdjmatch.jar
 
 # Add to PATH
 ENV PATH="/opt/quarto/1.6.42/bin:${PATH}"

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.