Reorganize to new targene-pipeline structure

.github/workflows/CI.yaml

@@ -0,0 +1,32 @@
+name: CI
+on:
+ - push
+ - pull_request
+concurrency:
+ # Skip intermediate builds: always.
+ # Cancel intermediate builds: only if it is a pull request build.
+ group: ${{ github.workflow }}-${{ github.ref }}
+ cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }}
+jobs:
+ test:
+ name: Test ${{ matrix.testrun }} -- ${{ github.event_name }}
+ runs-on: ubuntu-latest
+ strategy:
+ fail-fast: false
+ matrix:
+ testrun:
+ - "test1.py"
+ steps:
+ - uses: actions/checkout@v3
+ - name: Set up Python
+ uses: actions/setup-python@v3
+ with:
+ python-version: '3.11'
+ - name: Install Python dependencies
+ run: |
+ python -m pip install --upgrade pip
+ pip install -r test/requirements.txt
+ - name: Set up nextflow
+ uses: nf-core/setup-nextflow@v1.2.0
+ - name: Run tests
+ run: pytest test/${{ matrix.testrun }} 

assets/exclusion_regions_hg19.txt

@@ -0,0 +1,4 @@
+5 44000000 51500000 r1
+6 25000000 33500000 r2
+8 8000000 12000000 r3
+11 45000000 57000000 r4

assets/exclusion_regions_hg38.txt

@@ -0,0 +1,4 @@
+5 43999898 52204166 r1
+6 24999772 33532223 r2
+8 8142478 12142491 r3
+11 44978449 57232526 r4