SIRVs simulated perfect #41

	name: SIRVs simulated perfect

	on:
	workflow_dispatch:
	schedule:
	- cron: '0 12 * * 2'

	env:
	RUN_NAME: SIRVs.simulated
	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: 'SIRVs.simulated_perfect'
	if: always()
	shell: bash
	env:
	STEP_NAME: SIRVs.simulated_perfect
	run: \|
	export PATH=$PATH:${{env.BIN_PATH}}
	python3 ${{env.LAUNCHER}} ${{env.CFG_DIR}}/${{env.STEP_NAME}}.cfg -o ${{env.OUTPUT_BASE}}

	- name: 'IsoQuant: perfect reads with polyA'
	if: always()
	shell: bash
	env:
	STEP_NAME: SIRVs.simulated_perfect_polya
	run: \|
	export PATH=$PATH:${{env.BIN_PATH}}
	python3 ${{env.LAUNCHER}} ${{env.CFG_DIR}}/${{env.STEP_NAME}}.cfg -o ${{env.OUTPUT_BASE}}

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