Remove defaults channel from all modules and templates #5
Workflow file for this run
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# This is a workflow to run the metacells module | |
# | |
# 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 | |
# | |
# At initialization, only the manual trigger is active | |
name: Run metacells analysis module | |
env: | |
MODULE_PATH: analyses/metacells | |
AWS_DEFAULT_REGION: us-east-2 | |
concurrency: | |
# only one run per branch at a time | |
group: "run_metacells_${{ github.ref }}" | |
cancel-in-progress: true | |
on: | |
workflow_dispatch: | |
workflow_call: | |
pull_request: | |
branches: | |
- main | |
paths: | |
- "analyses/metacells/**" | |
jobs: | |
run-module: | |
if: github.repository_owner == 'AlexsLemonade' | |
runs-on: ubuntu-latest | |
defaults: | |
run: | |
shell: bash -el {0} | |
steps: | |
- name: Checkout repo | |
uses: actions/checkout@v4 | |
# Downloading just one sample for initial testing | |
- name: Download test data | |
run: ./download-data.py --test-data --format AnnData --sample SCPCS000001 | |
- name: Set up conda | |
uses: conda-incubator/setup-miniconda@v3 | |
- name: Install and activate locked conda environment | |
run: | | |
conda install conda-lock | |
conda-lock install --name test ${MODULE_PATH}/conda-lock.yml | |
- name: Run analysis module | |
run: | | |
cd ${MODULE_PATH} | |
# run module script here | |
bash run-metacells.sh |