Let me overlap #1158
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| on: | |
| push: | |
| branches: [ main ] | |
| paths-ignore: | |
| - '**/*.md' | |
| pull_request: | |
| branches: [ main ] | |
| paths-ignore: | |
| - '**/*.md' | |
| name: build and test | |
| jobs: | |
| build_and_test: | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Install required packages | |
| run: sudo apt-get update && sudo apt-get install -y | |
| git | |
| bash | |
| cmake | |
| make | |
| g++ | |
| python3-dev | |
| libatomic-ops-dev | |
| autoconf | |
| libgsl-dev | |
| zlib1g-dev | |
| libdeflate-dev | |
| libhts-dev | |
| samtools | |
| libjemalloc-dev | |
| bedtools | |
| - name: Init and update submodules | |
| run: git submodule update --init --recursive | |
| - name: Build wfmash | |
| run: cmake -H. -Bbuild -D CMAKE_BUILD_TYPE=Debug -DWFA_PNG_AND_TSV=ON && cmake --build build -- -j 2 | |
| - name: Test mapping coverage with 8 yeast genomes (PAF output) | |
| run: ASAN_OPTIONS=detect_leaks=1:symbolize=1 LSAN_OPTIONS=verbosity=0:log_threads=1 build/bin/wfmash data/scerevisiae8.fa.gz -p 95 -n 7 -m -L -Y '#' > scerevisiae8.paf; scripts/test.sh data/scerevisiae8.fa.gz.fai scerevisiae8.paf 0.92 | |
| - name: Test mapping+alignment with a subset of the LPA dataset (PAF output) | |
| run: ASAN_OPTIONS=detect_leaks=1:symbolize=1 LSAN_OPTIONS=verbosity=0:log_threads=1 build/bin/wfmash data/LPA.subset.fa.gz -n 10 -L > LPA.subset.paf && head LPA.subset.paf | |
| - name: Test mapping+alignment with a subset of the LPA dataset (SAM output) | |
| run: ASAN_OPTIONS=detect_leaks=1:symbolize=1 LSAN_OPTIONS=verbosity=0:log_threads=1 build/bin/wfmash data/LPA.subset.fa.gz -N -a -L > LPA.subset.sam && samtools view LPA.subset.sam -bS | samtools sort > LPA.subset.bam && samtools index LPA.subset.bam && samtools view LPA.subset.bam | head | cut -f 1-9 | |
| - name: Test mapping+alignment with short reads (500 bps) to a reference (SAM output) | |
| run: ASAN_OPTIONS=detect_leaks=1:symbolize=1 LSAN_OPTIONS=verbosity=0:log_threads=1 build/bin/wfmash data/reference.fa.gz data/reads.500bps.fa.gz -s 0.5k -N -a > reads.500bps.sam && samtools view reads.500bps.sam -bS | samtools sort > reads.500bps.bam && samtools index reads.500bps.bam && samtools view reads.500bps.bam | head | |
| - name: Test mapping+alignment with short reads (255bps) (PAF output) | |
| run: ASAN_OPTIONS=detect_leaks=1:symbolize=1 LSAN_OPTIONS=verbosity=0:log_threads=1 build/bin/wfmash data/reads.255bps.fa.gz -w 16 -s 100 -L > reads.255bps.paf && head reads.255bps.paf | |
| - name: Test input mapping functionality | |
| run: | | |
| # First generate mappings | |
| ASAN_OPTIONS=detect_leaks=1:symbolize=1 LSAN_OPTIONS=verbosity=0:log_threads=1 build/bin/wfmash data/scerevisiae8.fa.gz -p 95 -T S288C -Q SK1 -m >mappings.paf | |
| # Then align using the mappings | |
| ASAN_OPTIONS=detect_leaks=1:symbolize=1 LSAN_OPTIONS=verbosity=0:log_threads=1 build/bin/wfmash data/scerevisiae8.fa.gz -i mappings.paf > aligned.paf | |
| # Count lines in alignment file | |
| ALIGN_LINES=$(wc -l < aligned.paf) | |
| if [ $ALIGN_LINES -eq 0 ]; then | |
| echo "ERROR: Alignment file is empty" | |
| exit 1 | |
| else | |
| echo "Found $ALIGN_LINES alignments" | |
| fi | |
| - name: Install Rust and Cargo | |
| uses: actions-rs/toolchain@v1 | |
| with: | |
| toolchain: stable | |
| override: true | |
| - name: Install wgatools | |
| run: cargo install --git https://github.com/wjwei-handsome/wgatools.git | |
| - name: Install wgatools | |
| run: cargo install --git https://github.com/ekg/pafcheck.git | |
| - name: Run wfmash and generate PAF | |
| run: build/bin/wfmash -t 8 -T SGDref -Q S288C -Y '#' data/scerevisiae8.fa.gz > test.paf | |
| - name: check PAF coordinates and extended CIGAR validity | |
| run: pafcheck --query-fasta data/scerevisiae8.fa.gz --paf test.paf | |
| - name: Convert PAF to MAF using wgatools | |
| run: wgatools paf2maf --target data/scerevisiae8.fa.gz --query data/scerevisiae8.fa.gz test.paf > test.maf | |
| - name: Check if MAF file is not empty | |
| run: | | |
| if [ -s test.maf ]; then | |
| echo "MAF file is not empty. Test passed." | |
| else | |
| echo "MAF file is empty. Test failed." | |
| exit 1 | |
| fi |