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main.yml
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name: CI-main
on:
push:
branches:
- main
pull_request:
env:
SENTIEON_LICENSE: ${{ secrets.SENTIEON_LICENSE }}
SENTIEON_AUTH_MECH: "GitHub Actions - token"
ENCRYPTION_KEY: ${{ secrets.ENCRYPTION_KEY }}
LICENSE_MESSAGE: ${{ secrets.LICENSE_MESSAGE }}
jobs:
smoke:
strategy:
fail-fast: true
max-parallel: 1
matrix:
python-version: ["3.8", "3.12"]
poetry-version: ["1.5.1"]
sentieon-version: ["202308.01", "202308.02"]
os: [ubuntu-22.04] #, macos-latest, windows-latest]
runs-on: ${{ matrix.os }}
steps:
- uses: actions/checkout@v3
- uses: actions/setup-python@v4
with:
python-version: ${{ matrix.python-version }}
- name: Run image
uses: abatilo/actions-poetry@v2
with:
poetry-version: ${{ matrix.poetry-version }}
- name: Install the project dependencies
run: |
poetry config virtualenvs.in-project true
poetry install
- name: Install bcftools
run: |
sudo apt-get update
sudo apt-get install -y bcftools
- name: Install samtools
run: |
curl -L https://github.com/samtools/samtools/releases/download/1.19.2/samtools-1.19.2.tar.bz2 | tar -jxf -
cd samtools-1.19.2
./configure && sudo make install
- name: Install bedtools
run: |
sudo curl -L -o /usr/local/bin/bedtools "https://github.com/arq5x/bedtools2/releases/download/v2.31.0/bedtools.static"
sudo chmod ugo+x /usr/local/bin/bedtools
- name: Install sentieon
run: |
curl -L https://s3.amazonaws.com/sentieon-release/software/sentieon-genomics-$SENTIEON_VERSION.tar.gz | tar -zxf -
echo "SENTIEON_VERSION=$SENTIEON_VERSION" >> $GITHUB_ENV
echo "PATH=$(pwd)/sentieon-genomics-$SENTIEON_VERSION/bin:$PATH" >> $GITHUB_ENV
env:
SENTIEON_VERSION: ${{ matrix.sentieon-version }}
- name: Download long-read model
run: |
curl -L "https://s3.amazonaws.com/sentieon-release/other/DNAscopePacBio2.1.bundle" \
> "DNAscope PacBio2.1.bundle"
- name: Download short-read model
run: |
curl -L "https://s3.amazonaws.com/sentieon-release/other/DNAscopeIlluminaWGS2.0.bundle" \
> "DNAscope IlluminaWGS2.0.bundle"
- name: set SENTIEON_AUTH_DATA
run: |
SENTIEON_AUTH_DATA=$(python3 .github/scripts/license_message.py encrypt --key "$ENCRYPTION_KEY" --message "$LICENSE_MESSAGE")
echo "SENTIEON_AUTH_DATA=$SENTIEON_AUTH_DATA" >> $GITHUB_ENV
- name: Test spaces
run: |
gzip -dc tests/smoke/ref.fa.bgz > "tests/smoke/r ef.fa"
cp tests/smoke/ref.fa.fai "tests/smoke/r ef.fa.fai"
cp tests/smoke/sample.cram "tests/smoke/sam ple.cram"
cp tests/smoke/sample.cram.crai "tests/smoke/sam ple.cram.crai"
sentieon bwa index "tests/smoke/r ef.fa"
echo -e "chr20\t0\t2500" > "tests/smoke/r ef.bed"
- name: Smoke test - short-read
run: |
. .venv/bin/activate
sentieon-cli dnascope -t 1 -r "tests/smoke/r ef.fa" --pcr-free -g \
--duplicate-marking rmdup --consensus --align \
--input_ref "tests/smoke/r ef.fa" -i "tests/smoke/illumina.cram" \
-m "DNAscope IlluminaWGS2.0.bundle" "output_sr.vcf.gz"
if [ ! -f "output_sr.vcf.gz" -o ! -f "output_sr.g.vcf.gz" ]; then
exit 1
fi
- name: Smoke test - short-read fastq
run: |
. .venv/bin/activate
samtools fastq --reference "tests/smoke/r ef.fa" -1 sr_r1.fastq.gz \
-2 sr_r2.fastq.gz "tests/smoke/illumina.cram" > /dev/null
sentieon-cli dnascope -t 1 -r "tests/smoke/r ef.fa" --pcr-free \
--r1-fastq sr_r1.fastq.gz --r2-fastq sr_r2.fastq.gz \
--readgroups "@RG\tID:HG002-1\tSM:HG002" \
-m "DNAscope IlluminaWGS2.0.bundle" --assay WES \
--bed "tests/smoke/r ef.bed" "output_sr2.vcf.gz"
if [ ! -f "output_sr2.vcf.gz" ]; then
exit 1
fi
- name: Smoke test - long-read
run: |
. .venv/bin/activate
sentieon-cli dnascope-longread -t 1 -r "tests/smoke/r ef.fa" \
-i "tests/smoke/sam ple.cram" -m "DNAscope PacBio2.1.bundle" \
--repeat-model tests/smoke/sample_repeat.model -g \
-b "tests/smoke/diploid.bed" \
--haploid-bed "tests/smoke/haploid.bed" \
"output hifi.vcf.gz"
sentieon driver -r "tests/smoke/r ef.fa" -t 1 --algo GVCFtyper \
-v "output hifi.g.vcf.gz" output_hifi_gvcftyper.vcf.gz
if [ ! -f "output hifi.sv.vcf.gz" -o ! -f "output hifi.haploid.vcf.gz" ]; then
exit 1
fi
- name: Smoke test - gVCF
run: |
. .venv/bin/activate
sentieon-cli dnascope-longread --tech ONT -t 1 -r "tests/smoke/r ef.fa" \
-i "tests/smoke/sam ple.cram" -m "DNAscope PacBio2.1.bundle" \
--repeat-model tests/smoke/sample_repeat.model -g "output ont.vcf.gz"
sentieon driver -r "tests/smoke/r ef.fa" -t 1 --algo GVCFtyper \
-v "output ont.g.vcf.gz" output_hifi_gvcftyper.vcf.gz
if [ ! -f "output ont.sv.vcf.gz" ]; then
exit 1
fi
- name: Smoke test - realignment
run: |
. .venv/bin/activate
sentieon-cli dnascope-longread -t 1 -r "tests/smoke/r ef.fa" \
-i "tests/smoke/sam ple.cram" -m "DNAscope PacBio2.1.bundle" \
--repeat-model tests/smoke/sample_repeat.model --align \
--input_ref "tests/smoke/r ef.fa" "output realigned.vcf.gz"
if [ ! -f "output realigned.vcf.gz" -o ! -f "output realigned_mm2_sorted_0.cram" ]; then
exit 1
fi
- name: Smoke test - fastq
run: |
. .venv/bin/activate
samtools fastq --reference "tests/smoke/r ef.fa" \
"tests/smoke/sam ple.cram" | \
gzip -c > sample.fq.gz
sentieon-cli dnascope-longread -t 1 -r "tests/smoke/r ef.fa" \
--fastq sample.fq.gz --readgroups '@RG\tID:sample-1\tSM:sample' \
-m "DNAscope PacBio2.1.bundle" \
--repeat-model tests/smoke/sample_repeat.model "output fq.vcf.gz"
if [ ! -f "output fq.vcf.gz" -o ! -f "output fq_mm2_sorted_fq_0.cram" -o ! -f "output fq.sv.vcf.gz" ]; then
exit 1
fi