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Resume_tests.yml
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name: Resume option tests
on:
workflow_dispatch:
schedule:
- cron: '0 6 * * 2,5'
env:
RUN_NAME: Resume_tests
LAUNCHER: ${{github.workspace}}/tests/github/run_pipeline.py
CFG_DIR: /abga/work/andreyp/ci_isoquant/data
BIN_PATH: /abga/work/andreyp/ci_isoquant/bin/
OUTPUT_BASE: /abga/work/andreyp/ci_isoquant/output/${{github.ref_name}}/
concurrency:
group: ${{github.workflow}}
cancel-in-progress: false
jobs:
launch-runner:
runs-on:
labels: [isoquant]
name: 'Running IsoQuant and QC'
steps:
- name: 'Cleanup'
run: >
set -e &&
shopt -s dotglob &&
rm -rf *
- name: 'Checkout'
uses: actions/checkout@v3
with:
fetch-depth: 1
- name: 'Resume from assignment step'
if: always()
shell: bash
env:
STEP_NAME: RESUME1.SIRVs.R10
run: |
export PATH=$PATH:${{env.BIN_PATH}}
python3 ${{env.LAUNCHER}} ${{env.CFG_DIR}}/${{env.STEP_NAME}}.cfg -o ${{env.OUTPUT_BASE}}
- name: 'Resume from construction step'
if: always()
shell: bash
env:
STEP_NAME: RESUME2.SIRVs.R10
run: |
export PATH=$PATH:${{env.BIN_PATH}}
python3 ${{env.LAUNCHER}} ${{env.CFG_DIR}}/${{env.STEP_NAME}}.cfg -o ${{env.OUTPUT_BASE}}
- name: 'Resume from multimapper step'
if: always()
shell: bash
env:
STEP_NAME: RESUME3.SIRVs.R10
run: |
export PATH=$PATH:${{env.BIN_PATH}}
python3 ${{env.LAUNCHER}} ${{env.CFG_DIR}}/${{env.STEP_NAME}}.cfg -o ${{env.OUTPUT_BASE}}
- name: 'Resume from assignment step with additional options'
if: always()
shell: bash
env:
STEP_NAME: RESUME4.SIRVs.R10
run: |
export PATH=$PATH:${{env.BIN_PATH}}
python3 ${{env.LAUNCHER}} ${{env.CFG_DIR}}/${{env.STEP_NAME}}.cfg -o ${{env.OUTPUT_BASE}}
- name: 'Resume from assignment step with 2 files'
if: always()
shell: bash
env:
STEP_NAME: RESUME_GR1.SIRVs.R10
run: |
export PATH=$PATH:${{env.BIN_PATH}}
python3 ${{env.LAUNCHER}} ${{env.CFG_DIR}}/${{env.STEP_NAME}}.cfg -o ${{env.OUTPUT_BASE}}
- name: 'Resume from assignment step with TSV groups'
if: always()
shell: bash
env:
STEP_NAME: RESUME_GR2.SIRVs.R10
run: |
export PATH=$PATH:${{env.BIN_PATH}}
python3 ${{env.LAUNCHER}} ${{env.CFG_DIR}}/${{env.STEP_NAME}}.cfg -o ${{env.OUTPUT_BASE}}