script for pipeline to function with hg19_19 reference #46

	name: tests

	on:
	workflow_dispatch:
	push:
	branches:
	- master
	- main
	pull_request:
	branches_ignore: []

	jobs:
	Dry_Run_and_Lint:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v2
	- uses: docker://snakemake/snakemake:v5.24.2
	- name: Dry Run with test data
	run: \|
	docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 \
	/opt2/ervx run --input \
	/opt2/.tests/WT_S1.R1.fastq.gz /opt2/.tests/WT_S1.R2.fastq.gz \
	/opt2/.tests/WT_S2_R1.fastq.gz /opt2/.tests/WT_S2_R2.fastq.gz \
	/opt2/.tests/WT_S3_1.fastq.gz /opt2/.tests/WT_S3_2.fastq.gz \
	/opt2/.tests/WT_S4_R1.001.fastq.gz /opt2/.tests/WT_S4_R2.001.fastq.gz \
	--output /opt2/output --mode local --genome hg38_20 --dry-run
	- name: View the pipeline config file
	run: \|
	echo "Generated config file for pipeline...." && cat $PWD/output/config.json
	- name: Lint Workflow
	continue-on-error: true
	run: \|
	docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 snakemake --lint -s /opt2/output/workflow/Snakefile -d /opt2/output \|\| \
	echo 'There may have been a few warnings or errors. Please read through the log to determine if its harmless.'

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