Detect doublets in ScPCA data #21
Workflow file for this run
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# This is a workflow to run the doublet-detection module | |
# This module has both an renv and a conda environment | |
# | |
# Analysis modules are run based on three triggers: | |
# - Manual trigger | |
# - On pull requests where code in the module has changed | |
# - As a reusable workflow called from a separate workflow which periodically runs all modules | |
name: Run doublet-detection analysis module | |
env: | |
MODULE_PATH: analyses/doublet-detection | |
AWS_DEFAULT_REGION: us-east-1 | |
concurrency: | |
# only one run per branch at a time | |
group: doublet-detection-${{ github.ref }} | |
cancel-in-progress: true | |
on: | |
workflow_dispatch: | |
workflow_call: | |
pull_request: | |
branches: | |
- main | |
paths: | |
- analyses/doublet-detection/** | |
jobs: | |
run-module: | |
if: github.repository_owner == 'AlexsLemonade' | |
runs-on: ubuntu-latest | |
container: public.ecr.aws/openscpca/doublet-detection:latest | |
defaults: | |
run: | |
shell: bash -el {0} | |
steps: | |
- name: Checkout repo | |
uses: actions/checkout@v4 | |
- name: Download test data in SCE format | |
run: | | |
conda activate openscpca-doublet-detection | |
./download-data.py --test-data --format SCE | |
- name: Run doublet-detection module | |
run: | | |
projects=$(basename -a data/current/SCPCP*) | |
cd ${MODULE_PATH} | |
for project in $projects; do | |
bash run_doublet-detection-scpca.sh $project | |
done |