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Allow the PairedAssigner to use UMI pairs where one is absent #1093

Allow the PairedAssigner to use UMI pairs where one is absent

Allow the PairedAssigner to use UMI pairs where one is absent #1093

Workflow file for this run

name: unit tests
on: [push, pull_request]
jobs:
test:
runs-on: ubuntu-latest
steps:
- name: Checkout
uses: actions/checkout@v2
with:
fetch-depth: 0
lfs: true
- name: Checkout LFS objects
run: git lfs checkout
- name: Setup Scala
uses: olafurpg/setup-scala@v12
with:
java-version: [email protected]
- name: Unit Tests
run: |
set -e
sbt +clean coverage +test && sbt coverageReport coverageAggregate && (find $HOME/.sbt -name "*.lock" | xargs rm) && (find $HOME/.ivy2 -name "ivydata-*.properties" | xargs rm)
- name: Code Coverage
uses: codecov/[email protected]
with:
token: ${{ secrets.CODECOV_TOKEN }}
flags: unittests # optional
fail_ci_if_error: true # optional (default = false)
verbose: true # optional (default = false)
- name: Cache .ivy2
uses: actions/cache@v2
with:
path: ~/.ivy2
key: ${{ runner.os }}-ivy2-${{ hashFiles('**/build.sbt') }}
- name: Cache .sbt
uses: actions/cache@v2
with:
path: ~/.sbt
key: ${{ runner.os }}-sbt-${{ hashFiles('**/build.properties') }}
release:
if: github.repository == 'fulcrumgenomics/fgbio' && github.ref == 'refs/heads/main'
needs: test
runs-on: ubuntu-latest
env:
SONATYPE_USER: ${{ secrets.SONATYPE_USER }}
SONATYPE_PASS: ${{ secrets.SONATYPE_PASS }}
steps:
- uses: actions/checkout@v2
with:
fetch-depth: 0
- name: Setup Scala
uses: olafurpg/setup-scala@v12
with:
java-version: [email protected]
- name: Upload to Sonatype
run: |
sbt +publish