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Fix CRISPRessoPooled error reporting #30

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Fix CRISPRessoPooled error reporting

Fix CRISPRessoPooled error reporting #30

Workflow file for this run

.github/workflows/integration_tests.yml at 9b9b1e7
name: Run Integration Tests
on:
push:
pull_request:
types: [opened, reopened]
jobs:
build:
runs-on: ubuntu-latest
defaults:
run:
shell: bash -l {0}
env:
CRISPRESSO2_DIR: ${GITHUB_WORKSPACE}/../CRISPResso2_copy
strategy:
fail-fast: false
steps:
- uses: actions/checkout@v3
- name: Set up Conda
uses: conda-incubator/setup-miniconda@v2
with:
mamba-version: "*"
channels: conda-forge,bioconda,defaults
auto-activate-base: false
activate-environment: test_env
environment-file: .github/envs/test_env.yml
- name: Install dependencies
run: |
sudo apt-get update
sudo apt-get install -y gcc g++ bowtie2 samtools libsys-hostname-long-perl
pip install ydiff
- name: Create directory for files
run: |
mkdir ../CRISPResso2_copy
cp -r * ../CRISPResso2_copy
- name: Copy C2_tests repo
uses: actions/checkout@v3
with:
repository: edilytics/CRISPResso2_tests
token: ${{ secrets.ACCESS_CRISPRESSO2_TESTS }}
# ref: '<BRANCH_NAME>' // Use this to specify a branch other than master
- name: Run Basic
run: |
make basic test
- name: Run Params
if: success() || failure()
run: |
make params test
- name: Run Prime Editor
if: success() || failure()
run: |
make prime-editor test
- name: Run Batch
if: success() || failure()
run: |
make batch test
- name: Run Pooled
if: success() || failure()
run: |
make pooled test
- name: Run WGS
if: success() || failure()
run: |
make wgs test
- name: Run Compare
if: success() || failure()
run: |
make compare test