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test_on_push.yml
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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 -n 7 -m -L -Y '#' -T S288C -Q SK1 > 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
# Verify output has alignments (CIGAR strings)
grep -q "[0-9]\+M" aligned.paf || (echo "No alignments found in output" && exit 1)
- 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