Merge pull request #43 from UMCUGenetics/feature/refactor_kinship_pri…

…nt_to_write

Feature/refactor kinship print to write

.github/workflows/kinship_lint.yml

@@ -0,0 +1,17 @@
+name: Kinship Lint
+on:
+  pull_request:
+    paths: [Kinship/**]
+  push:
+    branches: [master, develop]
+    paths: [Kinship/**]
+
+jobs:
+  ruff:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: Kinship/
+    steps:
+      - uses: actions/checkout@v4
+      - uses: chartboost/ruff-action@v1

.github/workflows/kinship_test.yml

@@ -0,0 +1,63 @@
+# Source: https://github.com/marketplace/actions/install-poetry-action
+name: Kinship Test
+on:
+  pull_request:
+    paths: [Kinship/**]
+  push:
+    branches: [master, develop]
+    paths: [Kinship/**]
+
+jobs:
+  pytest:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: Kinship/
+    steps:
+      #----------------------------------------------
+      # check-out repo and set-up python
+      #----------------------------------------------
+      - name: Check out repository
+        uses: actions/checkout@v4
+      - name: Set up python
+        id: setup-python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11.5'
+      #----------------------------------------------
+      # install & configure poetry
+      #----------------------------------------------
+      - name: Install Poetry
+        uses: snok/install-poetry@v1
+        with:
+          version: 1.8.3
+          virtualenvs-create: true
+          virtualenvs-in-project: true
+          installer-parallel: true
+
+      #----------------------------------------------
+      # load cached venv if cache exists
+      #----------------------------------------------
+      - name: Load cached venv
+        id: cached-poetry-dependencies
+        uses: actions/cache@v4
+        with:
+          path: .venv
+          key: venv_kinship-${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/poetry.lock') }}
+      #----------------------------------------------
+      # install dependencies if cache does not exist
+      #----------------------------------------------
+      - name: Install dependencies
+        if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
+        run: poetry install --no-interaction --no-root
+      #----------------------------------------------
+      # install root project
+      #----------------------------------------------
+      - name: Install project
+        run: poetry install --no-interaction
+      #----------------------------------------------
+      # run pytest
+      #----------------------------------------------
+      - name: Run tests
+        run: |
+          poetry run pytest .

Kinship/Dockerfile

@@ -1,10 +1,44 @@
-FROM --platform=linux/amd64 continuumio/miniconda3
+################## BASE IMAGEs ######################
+FROM continuumio/miniconda3:24.5.0-0
 
-LABEL base_image="continuumio/miniconda3"
-LABEL version="1.0.0"
-LABEL extra.binaries="vcftools, plink, king"
+################## METADATA ######################
+LABEL base_image="continuumio/miniconda3:24.5.0-0"
+LABEL version="1.1.1"
+LABEL extra.binaries="vcftools, plink, king, pandas"
 
+################## INSTALLATIONS ######################
+# Use conda to install other dependencies.
 RUN conda config --add channels bioconda && \
     conda config --add channels conda-forge && \
     conda install -y vcftools=0.1.14 plink=1.90b4 king=2.2.7
 
+# Use poetry to install virtualenv.
+ENV POETRY_VERSION=1.8.3
+ENV POETRY_HOME=/opt/poetry
+ENV POETRY_VENV=/opt/poetry-venv
+
+# Tell Poetry where to place its cache and virtual environment
+ENV POETRY_CACHE_DIR=/tmp/poetry_cache
+
+# Do not ask any interactive question
+ENV POETRY_NO_INTERACTION=1
+
+# Make poetry create the virtual environment in the project's root
+# it gets named `.venv`
+ENV POETRY_VIRTUALENVS_IN_PROJECT=1
+ENV POETRY_VIRTUALENVS_CREATE=1
+
+# Set virtual_env variable
+ENV VIRTUAL_ENV=/.venv
+# Prepend virtual environments path
+ENV PATH="${VIRTUAL_ENV}/bin:${POETRY_VENV}/bin:${PATH}"
+
+# Creating a virtual environment just for poetry and install it with pip
+RUN python3 -m venv $POETRY_VENV \
+	&& $POETRY_VENV/bin/pip3 install poetry==${POETRY_VERSION}
+
+# Copy project requirement files here to ensure they will be cached.
+COPY pyproject.toml poetry.lock ./
+
+# Install dependencies.
+RUN --mount=type=cache,target=$POETRY_CACHE_DIR poetry install --without dev --no-interaction --no-cache

Kinship/Kinship.nf

@@ -1,7 +1,8 @@
 process Kinship {
     tag {"Kinship ${analysis_id}"}
     label 'Kinship'
-    container = 'docker.io/umcugenbioinf/kinship:1.0.0'
+    container = 'ghcr.io/umcugenetics/kinship:1.1.1'
+
     shell = ['/bin/bash', '-euo', 'pipefail']
 
     input:
@@ -17,6 +18,6 @@ process Kinship {
         plink --file out --make-bed --noweb
         king -b plink.bed --kinship
         cp king.kin0 ${analysis_id}.kinship
-        python ${projectDir}/CustomModules/Kinship/check_kinship.py ${analysis_id}.kinship ${ped_file} > ${analysis_id}.kinship_check.out
+        python ${projectDir}/CustomModules/Kinship/check_kinship.py ${analysis_id}.kinship ${ped_file} --output_prefix ${analysis_id} --output_path .
         """
-}
+}