add more workflows

.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"

.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

.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

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/.

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