add more workflows

regulatory-genomics · Oct 2, 2024 · 63accca · 63accca
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diff --git a/.github/workflows/nightly.yml b/.github/workflows/nightly.yml
@@ -0,0 +1,68 @@
+name: nightly-run
+
+on:
+  schedule:
+    - cron: '0 0 * * *' # Runs every day at midnight
+
+jobs:
+  check-for-new-commits:
+    runs-on: ubuntu-latest
+    outputs:
+      NEW_COMMITS: ${{ steps.check-commits.outputs.NEW_COMMITS }}
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Get latest commit SHA
+        id: get-latest-commit-sha
+        run: echo "LATEST_COMMIT_SHA=$(git rev-parse HEAD)" >> $GITHUB_ENV
+
+      - name: Check last run
+        id: check-commits
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          latest_run_commit_sha=$(curl --silent --header "Authorization: token $GITHUB_TOKEN" \
+              "https://api.github.com/repos/$GITHUB_REPOSITORY/actions/workflows/nightly.yml/runs?status=success&&per_page=1" \
+              | jq -r '.workflow_runs | first | .head_sha')
+          echo "Latest completed run was on commit: $latest_run_commit_sha"
+          echo "Current commit is: $LATEST_COMMIT_SHA"
+          if [ "$latest_run_commit_sha" != "$LATEST_COMMIT_SHA" ]; then
+            echo "NEW_COMMITS=true" >> "$GITHUB_OUTPUT"
+          else
+            echo "NEW_COMMITS=false" >> "$GITHUB_OUTPUT"
+          fi
+
+  build-wheel:
+    needs: check-for-new-commits
+    if : ${{ needs.check-for-new-commits.outputs.NEW_COMMITS == 'true' }}
+    uses: kaizhang/SnapATAC2/.github/workflows/wheels.yml@main
+
+  publish:
+    needs: build-wheel
+    runs-on: ubuntu-latest
+    steps:
+    - name: Download wheel files
+      uses: actions/download-artifact@v4
+      with:
+        path: dist
+        pattern: precellar-*
+        merge-multiple: true
+
+    - name: Delete Release
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      run: |
+        if gh release view nightly > /dev/null 2>&1; then
+          gh release delete nightly -y --cleanup-tag
+        fi
+
+    - name: Create nightly release
+      uses: ncipollo/release-action@v1
+      with:
+        allowUpdates: true
+        tag: nightly
+        name: Nightly Release
+        prerelease: true
+        removeArtifacts: true
+        artifacts: "dist/*.whl,dist/*.tar.gz"
diff --git a/.github/workflows/test_python.yml b/.github/workflows/test_python.yml
@@ -46,4 +46,8 @@ jobs:
       uses: actions/upload-artifact@v4
       with:
         name: wheel-files
-        path: ./wheel_files/precellar*.whl
+        path: ./wheel_files/precellar*.whl
+
+  build-wheel:
+    needs: build-and-test
+    uses: kaizhang/SnapATAC2/.github/workflows/wheels.yml@main
diff --git a/.github/workflows/wheels.yml b/.github/workflows/wheels.yml
@@ -0,0 +1,68 @@
+name: build-wheels
+on:
+  workflow_call
+
+jobs:
+  build_wheels:
+    name: Wheel on ${{ matrix.os }} for ${{ matrix.python_version }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-13, macos-14]
+        python_version: ["cp39-*", "cp310-*", "cp311-*", "cp312-*"]
+    env:
+       CIBW_BUILD_VERBOSITY: 1
+       CIBW_BEFORE_ALL_LINUX: >
+         curl https://sh.rustup.rs -sSf | sh -s -- -y && yum install -y openssl-devel zlib-devel
+
+       CIBW_ARCHS_LINUX: "auto64"
+       CIBW_ENVIRONMENT: 'PATH="$PATH:$HOME/.cargo/bin"'
+       CIBW_SKIP: "pp* *-win32 *-musllinux*"
+       CIBW_BUILD: ${{ matrix.python_version }}
+       #CIBW_TEST_REQUIRES: pytest hypothesis==6.72.4
+       #CIBW_TEST_COMMAND: "pytest {project}/snapatac2-python/tests"
+
+    steps:
+      - name: Checkout code
+        uses: nschloe/action-cached-lfs-checkout@v1
+
+      - uses: ./.github/actions/setup-rust
+
+      # Used to host cibuildwheel
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+
+      - name: Install cibuildwheel
+        run: python -m pip install cibuildwheel==2.20.0
+
+      - name: Build wheels
+        run: python -m cibuildwheel --output-dir wheelhouse python
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: precellar-${{ matrix.os }}-${{ strategy.job-index }}
+          path: ./wheelhouse/*.whl
+
+  make_sdist:
+    name: Build source distribution
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v4
+        name: Install Python
+        with:
+          python-version: '3.10'
+
+      - name: Install maturin
+        run: pip install maturin
+
+      - name: Build sdist
+        run: maturin sdist
+        working-directory: python
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: precellar-sdist
+          path: python/target/wheels/*.tar.gz
diff --git a/python/src/utils.rs b/python/src/utils.rs
@@ -21,7 +21,7 @@ use regex::Regex;
 ///     Extract barcodes from read names of BAM records using regular expressions.
 ///     Reguler expressions should contain exactly one capturing group 
 ///     (Parentheses group the regex between them) that matches
-///     the barcodes. For example, `barcode_regex="(..:..:..:..):\\\\w+$"`
+///     the barcodes. For example, `barcode_regex="(..:..:..:..):\\w+$"`
 ///     extracts `bd:69:Y6:10` from
 ///     `A01535:24:HW2MMDSX2:2:1359:8513:3458:bd:69:Y6:10:TGATAGGTTG`.
 ///     You can test your regex on this website: https://regex101.com/.

diff --git a/seqspec_templates/10x_atac.yaml b/seqspec_templates/10x_atac.yaml
@@ -0,0 +1,152 @@
+!Assay
+seqspec_version: 0.3.0
+assay_id: 10xATAC
+name: 10x-ATAC
+doi: https://www.10xgenomics.com/blog/demonstrated-protocol-for-nuclei-isolation-for-single-cell-atac-solution
+date: 19 October 2018
+description: Single Cell ATAC
+modalities:
+- atac
+lib_struct: https://teichlab.github.io/scg_lib_structs/methods_html/10xChromium_scATAC.html
+library_protocol: Custom
+library_kit: Custom
+sequence_protocol: Illumina
+sequence_kit: Custom
+sequence_spec:
+- !Read
+  read_id: R1
+  name: Read 1
+  modality: atac
+  primer_id: nextera_read1
+  min_len: 1
+  max_len: 98
+  strand: pos
+- !Read
+  read_id: I1
+  name: Index 1 (i7 index)
+  modality: atac
+  primer_id: nextera_read2
+  min_len: 8
+  max_len: 8
+  strand: pos
+- !Read
+  read_id: I2
+  name: Index 2 (i5 index)
+  modality: atac
+  primer_id: nextera_read1
+  min_len: 16
+  max_len: 16
+  strand: neg
+- !Read
+  read_id: R2
+  name: Read 2
+  modality: atac
+  primer_id: nextera_read2
+  min_len: 1
+  max_len: 98
+  strand: neg
+library_spec:
+- !Region
+  region_id: atac
+  region_type: atac
+  name: atac
+  sequence_type: joined
+  sequence: XXXXXXXXXXXXXXXXXXXXXXXXXXXXXNNNNNNNNNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAGXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXCTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG
+  min_len: 145
+  max_len: 1144
+  onlist: null
+  regions:
+  - !Region
+    region_id: illumina_p5
+    region_type: illumina_p5
+    name: Illumina P5
+    sequence_type: random
+    sequence: XXXXXXXXXXXXXXXXXXXXXXXXXXXXX
+    min_len: 29
+    max_len: 29
+    onlist: null
+    regions: null
+    parent_id: atac
+  - !Region
+    region_id: cell_bc
+    region_type: barcode
+    name: Cell Barcode
+    sequence_type: onlist
+    sequence: NNNNNNNNNNNNNNNN
+    min_len: 16
+    max_len: 16
+    onlist: !Onlist
+      file_id: 737K-cratac-v1.txt.gz
+      filename: 737K-cratac-v1.txt.gz
+      filetype: txt
+      filesize: 0
+      url: https://teichlab.github.io/scg_lib_structs/data/10X-Genomics/737K-cratac-v1.txt.gz
+      urltype: https
+      md5: null
+      location: remote
+    regions: null
+    parent_id: atac
+  - !Region
+    region_id: nextera_read1
+    region_type: nextera_read1
+    name: nextera_read1
+    sequence_type: fixed
+    sequence: TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG
+    min_len: 33
+    max_len: 33
+    onlist: null
+    regions: null
+    parent_id: atac
+  - !Region
+    region_id: gdna
+    region_type: gdna
+    name: gdna
+    sequence_type: random
+    sequence: XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
+    min_len: 1
+    max_len: 1000
+    onlist: null
+    regions: null
+    parent_id: atac
+  - !Region
+    region_id: nextera_read2
+    region_type: nextera_read2
+    name: nextera_read2
+    sequence_type: fixed
+    sequence: CTGTCTCTTATACACATCTCCGAGCCCACGAGAC
+    min_len: 34
+    max_len: 34
+    onlist: null
+    regions: null
+    parent_id: atac
+  - !Region
+    region_id: index7
+    region_type: index7
+    name: index7
+    sequence_type: onlist
+    sequence: NNNNNNNN
+    min_len: 8
+    max_len: 8
+    onlist: !Onlist
+      file_id: index7_onlist.txt
+      filename: index7_onlist.txt
+      filetype: ''
+      filesize: 0
+      url: ''
+      urltype: local
+      md5: null
+      location: local
+    regions: null
+    parent_id: atac
+  - !Region
+    region_id: illumina_p7
+    region_type: illumina_p7
+    name: Illumina P7
+    sequence_type: fixed
+    sequence: ATCTCGTATGCCGTCTTCTGCTTG
+    min_len: 24
+    max_len: 24
+    onlist: null
+    regions: null
+    parent_id: atac
+  parent_id: null