Merge pull request #10 from pdimens/dev

move dev to release
pdimens · Aug 24, 2023 · 621edca · 621edca
2 parents bba8b38 + 81f9106
commit 621edca
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diff --git a/.github/workflows/align.yml b/.github/workflows/align.yml
@@ -0,0 +1,78 @@
+name: Test Align
+
+on:
+  push:
+    branches:
+      - 'dev'
+    paths:
+      - 'rules/align-**.smk'
+      - '**align.py'
+      - 'reports/reportBwaGencov.Rmd'
+      - 'reports/reportEmaGencov.Rmd'
+      - 'reports/reportEmaCount.Rmd'
+      - 'reports/reportBxCount.Rmd'
+      - 'reports/reportBxStats.Rmd'
+      - 'reports/ilities/bxStats.py'
+      - 'utilities/countBX.py'
+      - 'utilities/makewindows.py'
+      - 'test/fastq/**'
+      - '**align.yml'
+
+  pull_request:
+    branches:
+      - 'dev'
+    paths:
+      - 'rules/align-**.smk'
+      - '**align.py'
+      - 'reports/reportBwaGencov.Rmd'
+      - 'reports/reportEmaGencov.Rmd'
+      - 'reports/reportEmaCount.Rmd'
+      - 'reports/reportBxCount.Rmd'
+      - 'reports/reportBxStats.Rmd'
+      - 'reports/ilities/bxStats.py'
+      - 'utilities/countBX.py'
+      - 'utilities/makewindows.py'
+      - 'test/fastq/**'
+      - '**align.yml'
+
+  schedule:
+    - cron: '0 0 * * *'
+
+env:
+  CACHE_NUMBER: 0  # increase to reset cache manually
+
+jobs:
+  build:
+    name: linux64
+    runs-on: ubuntu-latest
+    steps:
+      - name: checkout
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 1
+      - name: setup mamba
+        uses: mamba-org/setup-micromamba@v1
+        env:
+          ACTIONS_STEP_DEBUG: true
+        with:
+          init-shell: bash
+          generate-run-shell: true
+          environment-file: misc/harpyenv.yaml
+          cache-environment: true
+          post-cleanup: 'all'
+          log-level: error
+      - name: Install harpy
+        run: |
+          python3 -m pip install --upgrade build && python3 -m build
+          pip install dist/*.whl
+          misc/buildforCI.sh
+        shell: micromamba-shell {0}
+
+      - name: align bwa
+        shell: micromamba-shell {0}
+        run: harpy align --method bwa -d test/fastq -g test/genome/genome.fasta.gz -s "--show-failed-logs"
+        continue-on-error: true
+
+      - name: align ema
+        shell: micromamba-shell {0}
+        run: harpy align --method ema --ema-bins 20 -d test/fastq -g test/genome/genome.fasta.gz -s "--show-failed-logs"
diff --git a/.github/workflows/demux.yml b/.github/workflows/demux.yml
@@ -0,0 +1,58 @@
+name: Test Demultiplex
+
+on:
+  push:
+    branches:
+      - 'dev'
+    paths:
+      - 'rules/demultiplex**.smk'
+      - '**demultiplex.py'
+      - '**demuxGen1'
+      - '**demux.yml'
+      - 'BC_files.py'
+      - 'test/data/demux/**'
+
+  pull_request:
+    branches:
+    - 'dev'
+    paths:
+      - 'rules/demultiplex**.smk'
+      - '**demultiplex.py'
+      - '**demuxGen1'
+      - '**demux.yml'
+      - 'BC_files.py'
+      - 'test/data/demux/**'
+
+  schedule:
+    - cron: '0 0 * * *'
+
+env:
+  CACHE_NUMBER: 0  # increase to reset cache manually
+
+jobs:
+  build:
+    name: linux64
+    runs-on: ubuntu-latest
+    steps:
+      - name: checkout
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 1
+      - name: setup mamba
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          init-shell: bash
+          generate-run-shell: true
+          environment-file: misc/harpyenv.yaml
+          cache-environment: true
+          post-cleanup: 'all'
+      - name: Install harpy
+        run: |
+          python3 -m pip install --upgrade build && python3 -m build
+          pip install dist/*.whl
+          misc/buildforCI.sh
+        shell: micromamba-shell {0}
+
+      - name: Test harpy demux
+        run: harpy demultiplex --file test/demux/Undetermined_S0_L004_I1_001.fastq.gz --samplesheet test/demux/samples.schema
+        shell: micromamba-shell {0}
diff --git a/.github/workflows/impute.yml b/.github/workflows/impute.yml
@@ -0,0 +1,71 @@
+name: Test Impute
+
+on:
+  push:
+    branches:
+      - 'dev'
+    paths:
+      - 'rules/impute.smk'
+      - '**impute.py'
+      - 'test/bam/**'
+      - 'test/vcf/test.bcf'
+      - '**impute.yml'
+      - 'reports/reportImpute.Rmd'
+      - 'reports/reportStitch.Rmd'
+      - 'utilities/stitch_impute.R'
+
+  pull_request:
+    branches:
+      - 'dev'
+    paths:
+      - 'rules/impute.smk'
+      - '**impute.py'
+      - 'test/bam/**'
+      - 'test/vcf/test.bcf'
+      - '**impute.yml'
+      - 'reports/reportImpute.Rmd'
+      - 'reports/reportStitch.Rmd'
+      - 'utilities/stitch_impute.R'
+
+  schedule:
+    - cron: '0 0 * * *'
+
+env:
+  CACHE_NUMBER: 0  # increase to reset cache manually
+
+jobs:
+  build:
+    name: linux64
+    runs-on: ubuntu-latest
+    steps:
+      - name: checkout
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 1
+      - name: setup mamba
+        uses: mamba-org/setup-micromamba@v1
+        env:
+          ACTIONS_STEP_DEBUG: true
+        with:
+          init-shell: bash
+          generate-run-shell: true
+          environment-file: misc/harpyenv.yaml
+          cache-environment: true
+          post-cleanup: 'all'
+          log-level: error
+      - name: Install harpy
+        run: |
+          python3 -m pip install --upgrade build && python3 -m build
+          pip install dist/*.whl
+          misc/buildforCI.sh
+        shell: micromamba-shell {0}
+
+      - name: impute
+        shell: micromamba-shell {0}
+        run: harpy impute --vcf test/vcf/test.bcf -d test/bam -p test/stitch.params -s "--show-failed-logs"
+
+      - name: impute from vcf
+        shell: micromamba-shell {0}
+        run: |
+          rm -rf Impute
+          harpy impute --vcf-samples --vcf test/vcf/test.bcf -d test/bam -p test/stitch.params -s "--show-failed-logs"
diff --git a/.github/workflows/phase.yml b/.github/workflows/phase.yml
@@ -0,0 +1,78 @@
+name: Test Phase
+
+on:
+  push:
+    branches:
+      - 'dev'
+    paths:
+      - 'rules/phase-pop.smk'
+      - '**phase.py'
+      - 'test/bam/**'
+      - 'test/vcf/test.bcf'
+      - '**phase.yml'
+      - 'reports/reportHapCut2.Rmd'
+      - 'utilities/parsePhaseBlocks.py'
+      - 'utilities/summarizeHaplobocks.py'
+
+  pull_request:
+    branches:
+      - 'dev'
+    paths:
+      - 'rules/phase-pop.smk'
+      - '**phase.py'
+      - 'test/bam/**'
+      - 'test/vcf/test.bcf'
+      - '**phase.yml'
+      - 'reports/reportHapCut2.Rmd'
+      - 'utilities/parsePhaseBlocks.py'
+      - 'utilities/summarizeHaplobocks.py'
+
+  schedule:
+    - cron: '0 0 * * *'
+
+env:
+  CACHE_NUMBER: 0  # increase to reset cache manually
+
+
+jobs:
+  build:
+    name: linux64
+    runs-on: ubuntu-latest
+    steps:
+      - name: checkout
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 1
+      - name: setup mamba
+        uses: mamba-org/setup-micromamba@v1
+        env:
+          ACTIONS_STEP_DEBUG: true
+        with:
+          init-shell: bash
+          generate-run-shell: true
+          environment-file: misc/harpyenv.yaml
+          cache-environment: true
+          post-cleanup: 'all'
+          log-level: error
+      - name: Install harpy
+        run: |
+          python3 -m pip install --upgrade build && python3 -m build
+          pip install dist/*.whl
+          misc/buildforCI.sh
+        shell: micromamba-shell {0}
+
+      - name: phase
+        shell: micromamba-shell {0}
+        run: harpy phase --vcf test/vcf/test.bcf -d test/bam -s "--show-failed-logs"
+
+      - name: phase with indels
+        shell: micromamba-shell {0}
+        run: |
+          rm -rf Phase
+          harpy phase --vcf test/vcf/test.bcf -g test/genome/genome.fasta.gz -d test/bam -s "--show-failed-logs"
+
+      - name: phase from vcf
+        shell: micromamba-shell {0}
+        run: |
+          rm -rf Phase
+          harpy phase --vcf-samples --vcf test/vcf/test.bcf -d test/bam -s "--show-failed-logs"
diff --git a/.github/workflows/trim.yml b/.github/workflows/trim.yml
@@ -0,0 +1,54 @@
+name: Test Trim
+
+on:
+  push:
+    branches:
+      - 'dev'
+    paths:
+      - 'rules/trim.smk'
+      - '**trim.py'
+      - 'test/fastq/**'
+      - '**trim.yml'
+
+  pull_request:
+    branches:
+      - 'dev'
+    paths:
+      - 'rules/trim.smk'
+      - '**trim.py'
+      - 'test/fastq/**'
+      - '**trim.yml'
+
+  schedule:
+    - cron: '0 0 * * *'
+
+env:
+  CACHE_NUMBER: 0  # increase to reset cache manually
+
+jobs:
+  build:
+    name: linux64
+    runs-on: ubuntu-latest
+    steps:
+      - name: checkout
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 1
+      - name: setup mamba
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          init-shell: bash
+          generate-run-shell: true
+          environment-file: misc/harpyenv.yaml
+          cache-environment: true
+          post-cleanup: 'all'
+      - name: Install harpy
+        run: |
+          python3 -m pip install --upgrade build && python3 -m build
+          pip install dist/*.whl
+          misc/buildforCI.sh
+        shell: micromamba-shell {0}
+
+      - name: Test harpy trim
+        run: harpy trim -d test/fastq
+        shell: micromamba-shell {0}