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Read grouping tests #117

Read grouping tests

Read grouping tests #117

Workflow file for this run

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}}