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Update the gvcf_combine script #3

Update the gvcf_combine script

Update the gvcf_combine script #3

Workflow file for this run

name: CI-main
on:
push:
branches:
- main
pull_request:
env:
SENTIEON_VERSION: "202308.01"
jobs:
smoke:
strategy:
fail-fast: true
matrix:
python-version: ["3.12"]
poetry-version: ["1.5.1"]
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: ${{ matrix.poetry-version }}
- name: Install the project dependencies
run: |
poetry config virtualenvs.in-project true
poetry install
- name: Install bcftools
run: |
sudo apt-get update
sudo apt-get install -y bcftools
- name: Install bedtools
run: |
sudo curl -L -o /usr/local/bin/bedtools "https://github.com/arq5x/bedtools2/releases/download/v2.31.0/bedtools.static"
sudo chmod ugo+x /usr/local/bin/bedtools
- name: Install sentieon
run: |
curl -L https://s3.amazonaws.com/sentieon-release/software/sentieon-genomics-$SENTIEON_VERSION.tar.gz | tar -zxf -
- name: Download model
run: curl -LO "https://s3.amazonaws.com/sentieon-release/other/DNAscopePacBio2.0.bundle"
- name: Smoke test
run: |
SENTIEON_AUTH_DATA=$(python3 .github/scripts/license_message.py encrypt --key "$ENCRYPTION_KEY" --message "$LICENSE_MESSAGE")
export SENTIEON_AUTH_DATA
. .venv/bin/activate
export PATH=$(pwd)/sentieon-genomics-$SENTIEON_VERSION/bin:$PATH
gzip -dc tests/smoke/ref.fa.bgz > tests/smoke/ref.fa
sentieon-cli dnascope-longread -r tests/smoke/ref.fa -i tests/smoke/sample.cram -m DNAscopePacBio2.0.bundle --repeat-model tests/smoke/sample_repeat.model -g output_hifi.vcf.gz
sentieon driver -r tests/smoke/ref.fa --algo GVCFtyper -v output_hifi.g.vcf.gz output_hifi_gvcftyper.vcf.gz
sentieon-cli dnascope-longread --tech ONT -r tests/smoke/ref.fa -i tests/smoke/sample.cram -m DNAscopePacBio2.0.bundle --repeat-model tests/smoke/sample_repeat.model -g output_ont.vcf.gz
sentieon driver -r tests/smoke/ref.fa --algo GVCFtyper -v output_ont.g.vcf.gz output_hifi_gvcftyper.vcf.gz
env:
SENTIEON_LICENSE: ${{ secrets.SENTIEON_LICENSE }}
SENTIEON_AUTH_MECH: "GitHub Actions - token"
ENCRYPTION_KEY: ${{ secrets.ENCRYPTION_KEY }}
LICENSE_MESSAGE: ${{ secrets.LICENSE_MESSAGE }}