Add multi-ref scheme selection support

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

@@ -0,0 +1,39 @@
+name: quay_build_push
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  docker:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Docker meta
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: quay.io/artic-network/fieldbioinformatics
+          flavor: |
+            latest=true
+          tags: |
+            type=semver,pattern={{version}}
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v3
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+      - name: Login to Docker Hub
+        uses: docker/login-action@v3
+        with:
+          registry: quay.io
+          username: ${{ secrets.QUAY_USERNAME }}
+          password: ${{ secrets.QUAY_PASSWORD }}
+      - name: Build and push
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          platforms: linux/amd64
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}

.github/workflows/unittests.yml

@@ -0,0 +1,45 @@
+name: fieldbioinformatics_unit_tests
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+    steps:
+      - uses: actions/checkout@v3
+      - uses: mamba-org/setup-micromamba@v1
+        name: Setup dependencies
+        with:
+          environment-file: environment.yml
+          init-shell: >-
+            bash
+          cache-environment: true
+          post-cleanup: "all"
+
+      - name: Pip install artic
+        run: |
+          python3 -m pip install -e .
+        shell: micromamba-shell {0}
+
+      - name: Run unit tests
+        run: |
+          pytest -s tests/*_unit_test.py
+        shell: micromamba-shell {0}
+
+      - name: Run medaka test
+        run: |
+          ./test-runner.sh medaka
+        shell: micromamba-shell {0}
+
+      - name: Run clair3 test
+        run: |
+          ./test-runner.sh clair3
+        shell: micromamba-shell {0}
+
+      - name: Run minion_validator tests
+        run: |
+          pytest -s tests/minion_validator.py
+        shell: micromamba-shell {0}
+

.gitignore

@@ -26,6 +26,14 @@ dist/
 
 # test data
 *.index*
-CVR1/
-NRW01/
-SP1/
+CVR1.*
+NRW01.*
+SP1.*
+MT007544*
+tmp/
+test-data/CVR1/
+test-data/NRW01/
+test-data/SP1/
+test-data/MT007544/
+rg_*
+primer-schemes/

Dockerfile

@@ -0,0 +1,31 @@
+FROM mambaorg/micromamba:1.5.8
+
+COPY . ./fieldbioinformatics/
+
+USER root
+
+RUN apt-get update && apt-get install -y --no-install-recommends build-essential wget procps
+
+USER $MAMBA_USER
+
+COPY --chown=$MAMBA_USER:$MAMBA_USER environment.yml /tmp/env.yml
+
+RUN sed -i 's/name: artic/name: base/' /tmp/env.yml
+
+RUN micromamba install --yes --file /tmp/env.yml && \
+    micromamba clean --all --yes
+
+ARG MAMBA_DOCKERFILE_ACTIVATE=1
+
+USER root
+
+RUN python3 -m pip install ./fieldbioinformatics
+
+RUN pip uninstall -y tensorflow keras pyabpoa \
+  && micromamba install -y -c conda-forge -c bioconda tensorflow=2.11 keras=2.11
+
+USER $MAMBA_USER
+
+ENTRYPOINT ["/usr/local/bin/_entrypoint.sh"]
+
+CMD ["/bin/bash"]

README.md

@@ -27,34 +27,34 @@ Features include:
 
 There are **2 workflows** baked into this pipeline, one which uses signal data (via [nanopolish](https://github.com/jts/nanopolish)) and one that does not (via [medaka](https://github.com/nanoporetech/medaka)).
 
-## Installation
+<!-- ## Installation
 
 ### Via conda
 
 ```sh
 conda install -c bioconda -c conda-forge artic
 ```
 
-If conda reports that nothing provides particular packages when running the above command ensure your `channel_priority` is set to `flexible` using the following command:
-
-```sh
-conda config --set channel_priority false
-```
+Please make sure you are using either mamba or conda version >= 23.10.0 where libmamba solver was made the default conda solver. -->
 
 ### Via source
 
 #### 1. downloading the source:
 
-Download a [release](https://github.com/artic-network/fieldbioinformatics/releases) or use the latest master (which tracks the current release):
+<!-- Download a [release](https://github.com/artic-network/fieldbioinformatics/releases) or use the latest master (which tracks the current release): -->
+
+Clone the repository then checkout the 1.4.0-dev branch to test the 1.4.0 pre-release.
 
 ```sh
 git clone https://github.com/artic-network/fieldbioinformatics
 cd fieldbioinformatics
+git checkout 1.4.0-dev
 ```
 
 #### 2. installing dependencies:
 
-The `artic pipeline` has several [software dependencies](https://github.com/artic-network/fieldbioinformatics/blob/master/environment.yml). You can solve these dependencies using the minimal conda environment we have provided:
+The `artic pipeline` has several [software dependencies](https://github.com/artic-network/fieldbioinformatics/blob/master/environment.yml). You can solve these dependencies using the minimal conda environment we have provided, Please make sure you are using either mamba or conda version >= 23.10.0 where libmamba solver was made the default conda solver.
+:
 
 ```sh
 conda env create -f environment.yml
@@ -64,7 +64,7 @@ conda activate artic
 #### 3. installing the pipeline:
 
 ```sh
-python setup.py install
+pip install .
 ```
 
 #### 4. testing the pipeline:

artic/.gitignore

@@ -0,0 +1,3 @@
+# pixi environments
+.pixi
+*.egg-info