Read grouping tests #120
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name: Read grouping tests | |
on: | |
workflow_dispatch: | |
schedule: | |
- cron: '0 2 * * 0,4' | |
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: ${{github.workflow}} | |
cancel-in-progress: false | |
jobs: | |
launch-runner: | |
runs-on: | |
labels: [isoquant] | |
name: 'Running IsoQuant and QC' | |
steps: | |
- name: 'Cleanup' | |
run: > | |
set -e && | |
shopt -s dotglob && | |
rm -rf * | |
- name: 'Checkout' | |
uses: actions/checkout@v3 | |
with: | |
fetch-depth: 1 | |
- name: 'Grouping by BAM tag' | |
if: always() | |
shell: bash | |
env: | |
STEP_NAME: GROUP1.TAG.SIRVs.R10 | |
run: | | |
export PATH=$PATH:${{env.BIN_PATH}} | |
python3 ${{env.LAUNCHER}} ${{env.CFG_DIR}}/${{env.STEP_NAME}}.cfg -o ${{env.OUTPUT_BASE}} | |
- name: 'Grouping by TSV file' | |
if: always() | |
shell: bash | |
env: | |
STEP_NAME: GROUP2.TSV.SIRVs.R10 | |
run: | | |
export PATH=$PATH:${{env.BIN_PATH}} | |
python3 ${{env.LAUNCHER}} ${{env.CFG_DIR}}/${{env.STEP_NAME}}.cfg -o ${{env.OUTPUT_BASE}} | |
- name: 'Grouping by read id' | |
if: always() | |
shell: bash | |
env: | |
STEP_NAME: GROUP3.READID.SIRVs.R10 | |
run: | | |
export PATH=$PATH:${{env.BIN_PATH}} | |
python3 ${{env.LAUNCHER}} ${{env.CFG_DIR}}/${{env.STEP_NAME}}.cfg -o ${{env.OUTPUT_BASE}} | |
- name: 'Grouping by file name' | |
if: always() | |
shell: bash | |
env: | |
STEP_NAME: GROUP4.FILES.SIRVs.R10 | |
run: | | |
export PATH=$PATH:${{env.BIN_PATH}} | |
python3 ${{env.LAUNCHER}} ${{env.CFG_DIR}}/${{env.STEP_NAME}}.cfg -o ${{env.OUTPUT_BASE}} | |
- name: 'Grouping by CSV file' | |
if: always() | |
shell: bash | |
env: | |
STEP_NAME: GROUP5.CSV.SIRVs.R10 | |
run: | | |
export PATH=$PATH:${{env.BIN_PATH}} | |
python3 ${{env.LAUNCHER}} ${{env.CFG_DIR}}/${{env.STEP_NAME}}.cfg -o ${{env.OUTPUT_BASE}} | |