Initial commit: FlowDock pipeline configured for WES execution

.github/workflows/code-quality-main.yaml

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+# Same as `code-quality-pr.yaml` but triggered on commit to main branch
+# and runs on all files (instead of only the changed ones)
+
+name: Code Quality Main
+
+on:
+  push:
+    branches: [main]
+
+jobs:
+  code-quality:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+
+      - name: Run pre-commits
+        uses: pre-commit/action@v2.0.3

.github/workflows/code-quality-pr.yaml

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+# This workflow finds which files were changed, prints them,
+# and runs `pre-commit` on those files.
+
+# Inspired by the sktime library:
+# https://github.com/alan-turing-institute/sktime/blob/main/.github/workflows/test.yml
+
+name: Code Quality PR
+
+on:
+  pull_request:
+    branches: [main, "release/*", "dev"]
+
+jobs:
+  code-quality:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+
+      - name: Find modified files
+        id: file_changes
+        uses: trilom/file-changes-action@v1.2.4
+        with:
+          output: " "
+
+      - name: List modified files
+        run: echo '${{ steps.file_changes.outputs.files}}'
+
+      - name: Run pre-commits
+        uses: pre-commit/action@v2.0.3
+        with:
+          extra_args: --files ${{ steps.file_changes.outputs.files}}

.github/workflows/release-drafter.yml

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+name: Release Drafter
+
+on:
+  push:
+    # branches to consider in the event; optional, defaults to all
+    branches:
+      - main
+
+permissions:
+  contents: read
+
+jobs:
+  update_release_draft:
+    permissions:
+      # write permission is required to create a github release
+      contents: write
+      # write permission is required for autolabeler
+      # otherwise, read permission is required at least
+      pull-requests: write
+
+    runs-on: ubuntu-latest
+
+    steps:
+      # Drafts your next Release notes as Pull Requests are merged into "master"
+      - uses: release-drafter/release-drafter@v5
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/test.yml

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+name: Tests
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main, "release/*", "dev"]
+
+jobs:
+  run_tests_ubuntu:
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ["ubuntu-latest"]
+        python-version: ["3.8", "3.9", "3.10"]
+
+    timeout-minutes: 20
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v3
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          conda env create -f environment.yml
+          python -m pip install --upgrade pip
+          pip install pytest
+          pip install sh
+
+      - name: List dependencies
+        run: |
+          python -m pip list
+
+      - name: Run pytest
+        run: |
+          pytest -v
+
+  run_tests_macos:
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ["macos-latest"]
+        python-version: ["3.8", "3.9", "3.10"]
+
+    timeout-minutes: 20
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v3
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          conda env create -f environment.yml
+          python -m pip install --upgrade pip
+          pip install pytest
+          pip install sh
+
+      - name: List dependencies
+        run: |
+          python -m pip list
+
+      - name: Run pytest
+        run: |
+          pytest -v
+
+  run_tests_windows:
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ["windows-latest"]
+        python-version: ["3.8", "3.9", "3.10"]
+
+    timeout-minutes: 20
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v3
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          conda env create -f environment.yml
+          python -m pip install --upgrade pip
+          pip install pytest
+
+      - name: List dependencies
+        run: |
+          python -m pip list
+
+      - name: Run pytest
+        run: |
+          pytest -v
+
+  # upload code coverage report
+  code-coverage:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.10"
+
+      - name: Install dependencies
+        run: |
+          conda env create -f environment.yml
+          python -m pip install --upgrade pip
+          pip install pytest
+          pip install pytest-cov[toml]
+          pip install sh
+
+      - name: Run tests and collect coverage
+        run: pytest --cov flowdock # NEEDS TO BE UPDATED WHEN CHANGING THE NAME OF "src" FOLDER
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v3