Remove Strelka and Mutect2 from somatic variant calling (#513)

* remove strelka and mutect2 * coveralls * stepS * test only for certain path * refactor env * remove cython * coveralls version unlock * remove --user from pip install * remove unused run * pip as module * remove activate * put activate back * good old source activate instead of conda * login bash * proper py.test * test help * get germline dynamic * remove unused lines * replace coveralls with codecov * codecov simpler
Clinical-Genomics · Nov 23, 2020 · 58c17b2 · 58c17b2
1 parent 6cf6c66
commit 58c17b2
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Showing 6 changed files with 75 additions and 23 deletions.
diff --git a/.github/workflows/docker_build_test.yml b/.github/workflows/docker_build_test.yml
@@ -8,6 +8,9 @@ on:
       - develop
     tags-ignore:
       - "**"
+    paths:
+      - 'BALSAMIC/containers/**'
+
 
 jobs:
   main:

diff --git a/.github/workflows/pytest_and_coveralls.yml b/.github/workflows/pytest_and_coveralls.yml
@@ -0,0 +1,59 @@
+name: PyTest and Coveralls
+
+on: ["push", "pull_request"]
+
+jobs:
+  pytest_coveralls:
+    name: run PyTest
+    runs-on: ubuntu-18.04
+    strategy:
+      fail-fast: false 
+      matrix: 
+        python-version: [3.6]
+
+    steps:
+      # Checkout BALSAMIC
+      - name: Git checkout
+        id: git_checkout
+        uses: actions/checkout@v2
+
+      # Get branch name
+      - name: Get branch name
+        id: get_branch_name
+        shell: bash
+        run: echo "##[set-output name=branch;]$(echo ${GITHUB_REF##*/})"
+
+      # Conda env create
+      - name: setup conda
+        id: setup_conda
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: balsamic
+          environment-file: BALSAMIC/conda/balsamic.yaml
+          python-version: ${{ matrix.python-version }} 
+
+      # Install BALSAMIC
+      - name: Install BALSAMIC
+        id: install_balsamic
+        shell: bash -l {0}
+        run: |
+          conda activate balsamic
+          pip install --no-cache-dir -r requirements-dev.txt -r requirements.txt
+          pip install -e .
+
+      # Run PyTest
+      - name: Run PyTest
+        id: pytest
+        shell: bash -l {0}
+        run: |
+          conda activate balsamic
+          py.test --cov-report=xml --cov=BALSAMIC -rsxv tests/*
+
+      # Run Codecov 
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v1
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          file: ./coverage.xml
+          flags: unittests
+          fail_ci_if_error: true
diff --git a/BALSAMIC/utils/constants.py b/BALSAMIC/utils/constants.py
@@ -79,24 +79,12 @@
         "analysis_type": ["paired", "single"],
         "workflow_solution": ["BALSAMIC"]
     },
-    "mutect": {
-        "mutation": "somatic",
-        "type": "SNV",
-        "analysis_type": ["paired", "single"],
-        "workflow_solution": ["BALSAMIC"]
-    },
     "vardict": {
         "mutation": "somatic",
         "type": "SNV",
         "analysis_type": ["paired", "single"],
         "workflow_solution": ["BALSAMIC"]
     },
-    "strelka": {
-        "mutation": "somatic",
-        "type": "SNV",
-        "analysis_type": ["paired"],
-        "workflow_solution": ["BALSAMIC"]
-    },
     "manta_germline": {
         "mutation": "germline",
         "type": "SV",
@@ -109,12 +97,6 @@
         "analysis_type": ["paired", "single"],
         "workflow_solution": ["BALSAMIC"]
     },
-    "strelka_germline": {
-        "mutation": "germline",
-        "type": "SNV",
-        "analysis_type": ["paired", "single"],
-        "workflow_solution": ["BALSAMIC"]
-    }
 }
 
 # Minimum required QC-values from HS metrics to be able to pass analysis

diff --git a/BALSAMIC/utils/models.py b/BALSAMIC/utils/models.py
@@ -148,15 +148,12 @@ class VCFModel(BaseModel):
     tnsnv: VarcallerAttribute
     manta: VarcallerAttribute
     cnvkit: VarcallerAttribute
-    mutect: VarcallerAttribute
     vardict: VarcallerAttribute
-    strelka: VarcallerAttribute
     tnscope: VarcallerAttribute
     dnascope: VarcallerAttribute
     tnhaplotyper: VarcallerAttribute
     manta_germline: VarcallerAttribute
     haplotypecaller: VarcallerAttribute
-    strelka_germline: VarcallerAttribute
 
 
 class AnalysisModel(BaseModel):

diff --git a/BALSAMIC/workflows/balsamic.smk b/BALSAMIC/workflows/balsamic.smk
@@ -125,7 +125,18 @@ else:
         "snakemake_rules/variant_calling/germline.rule",
         "snakemake_rules/variant_calling/split_bed.rule"
     ]
-    germline_caller = ["haplotypecaller", "strelka_germline", "manta_germline"]
+
+    germline_caller_SNV = get_variant_callers(config=config, analysis_type="paired",
+                                              workflow_solution="BALSAMIC",
+                                              mutation_type="SNV",
+                                              mutation_class="germline")
+    germline_caller_SV = get_variant_callers(config=config, analysis_type="paired",
+                                             workflow_solution="BALSAMIC",
+                                             mutation_type="SV",
+                                             mutation_class="germline")
+
+    germline_caller = germline_caller_SNV + germline_caller_SV
+
 
     if sentieon:
         germline_caller.append("dnascope")

diff --git a/requirements-dev.txt b/requirements-dev.txt
@@ -1,4 +1,4 @@
 pytest>=3.7.1
 pytest-cov==2.8.1
-coveralls==2.0.0
+coveralls
 pylint
-Original file line number
+Diff line change
@@ Expand Up / @@ -8,6 +8,9 @@ on: @@
           - develop
         tags-ignore:
           - "**"
+        paths:
+          - 'BALSAMIC/containers/**'
     jobs:
       main:
@@ Expand Down @@