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ci.yml
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name: ci
on:
push:
branches:
- '*'
pull_request:
branches:
- main
jobs:
cell_state_comparison:
runs-on: ubuntu-20.04
steps:
- name: Checkout SCUREL repository
uses: actions/checkout@v2
- name: Setup miniconda & SCUREL main env
uses: conda-incubator/setup-miniconda@v2
with:
python-version: 3.6.7
miniconda-version: 4.7.12
auto-update-conda: false
environment-file: install/scurel.yaml
activate-environment: scurel
auto-activate-base: false
- name: Display all miniconda & env info
shell: bash -l {0}
run: |
conda info -a
conda list
- name: Run snakemake rulegraph
shell: bash -l {0}
run: bash build_rulegraph.sh .test/integration-dry/cell_state_comparison_config.yaml
- name: Build snakemake DAG
shell: bash -l {0}
run: bash build_dag.sh .test/integration-dry/cell_state_comparison_config.yaml
- name: Build conda envs for specific rules
shell: bash -l {0}
run: snakemake --configfile .test/integration-dry/cell_state_comparison_config.yaml --use-conda --create-envs-only
- name: snakemake --dryrun
shell: bash -l {0}
run: bash exe_dry.sh .test/integration-dry/cell_state_comparison_config.yaml
- name: snakemake --dryrun test data
shell: bash -l {0}
run: bash exe_dry.sh .test/integration/cell_state_comparison.yaml
- name: snakemake run test data
shell: bash -l {0}
run: bash exe_snakemake_local.sh .test/integration/cell_state_comparison.yaml
cell_type_comparison:
runs-on: ubuntu-20.04
steps:
- name: Checkout SCUREL repository
uses: actions/checkout@v2
- name: Setup miniconda & SCUREL main env
uses: conda-incubator/setup-miniconda@v2
with:
python-version: 3.6.7
miniconda-version: 4.7.12
auto-update-conda: false
environment-file: install/scurel.yaml
activate-environment: scurel
auto-activate-base: false
- name: Display all miniconda & env info
shell: bash -l {0}
run: |
conda info -a
conda list
- name: Run snakemake rulegraph
shell: bash -l {0}
run: bash build_rulegraph.sh .test/integration-dry/cell_type_comparison_config.yaml
- name: Build snakemake DAG
shell: bash -l {0}
run: bash build_dag.sh .test/integration-dry/cell_type_comparison_config.yaml
- name: Build conda envs for specific rules
shell: bash -l {0}
run: snakemake --configfile .test/integration-dry/cell_type_comparison_config.yaml --use-conda --create-envs-only
- name: snakemake --dryrun
shell: bash -l {0}
run: bash exe_dry.sh .test/integration-dry/cell_type_comparison_config.yaml
- name: snakemake --dryrun test data
shell: bash -l {0}
run: bash exe_dry.sh .test/integration/cell_type_comparison.yaml
- name: snakemake run test data
shell: bash -l {0}
run: bash exe_snakemake_local.sh .test/integration/cell_type_comparison.yaml