Log and benchmark fixes #65
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# This is a basic workflow adapted from the default Action worflow | |
name: ARPEGGIO_run | |
# Controls when the action will run. Triggers the workflow on push or pull request | |
# events but only for the master branch. Added trigger to publishhed and created | |
# releases as well | |
on: | |
pull_request: | |
branches: [ master ] | |
release: | |
types: [ published, created ] | |
# The workflow will have three jobs: running the main ARPEGGIO mode, linting and trying additional configs | |
jobs: | |
# Name of the job | |
run-worfklow: | |
# The type of runner that the job will run on | |
runs-on: ubuntu-latest | |
# Steps represent a sequence of tasks that will be executed as part of the job | |
steps: | |
- uses: actions/checkout@v3 | |
# Run default snakemake | |
- uses: snakemake/snakemake-github-action@v1 | |
with: | |
directory: '.' | |
args: '--cores 1 --use-conda' | |
run-linting: | |
# The type of runner that the job will run on | |
runs-on: ubuntu-latest | |
# Steps represent a sequence of tasks that will be executed as part of the job | |
steps: | |
- uses: actions/checkout@v3 | |
# Run default snakemake | |
- uses: snakemake/snakemake-github-action@v1 | |
with: | |
directory: '.' | |
args: '--lint' | |
run-modes: | |
# The type of runner that the job will run on | |
runs-on: ubuntu-latest | |
# Steps represent a sequence of tasks that will be executed as part of the job | |
steps: | |
- uses: actions/checkout@v3 | |
# Run snakemake diploid only mode paired-end reads | |
- name: run-ARPEGGIO-dp-PE | |
uses: snakemake/snakemake-github-action@v1 | |
with: | |
directory: '.' | |
args: '--configfile example/additional_config/config_dp_PE.yaml -n' | |
# Run snakemake diploid only mode single-end reads | |
- name: run-ARPEGGIO-dp-SE | |
uses: snakemake/snakemake-github-action@v1 | |
with: | |
directory: '.' | |
args: '--configfile example/additional_config/config_dp_SE.yaml -n' | |
# Run snakemake polyploid only mode paired-end reads | |
- name: run-ARPEGGIO-pp-PE | |
uses: snakemake/snakemake-github-action@v1 | |
with: | |
directory: '.' | |
args: '--configfile example/additional_config/config_pp_PE.yaml -n' | |
# Run snakemake polyploid only mode single-end reads | |
- name: run-ARPEGGIO-pp-SE | |
uses: snakemake/snakemake-github-action@v1 | |
with: | |
directory: '.' | |
args: '--configfile example/additional_config/config_pp_SE.yaml -n' |