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Alex Kanitz authored
`README.md` file describes - aim and background of the project (including the workflow DAG representation) - how to install requirements (including setting up a `conda` environment for the project) - how to execute the workflow run integration test - how to run the workflow on your own samples (including how to auto-generate required params from LabKey metadata) Additional minor changes: - minor changes in various test and related files, including updates of paths - root directory now includes subdirectory `runs/` for a user's workflow runs (contents not version-controlled)
Alex Kanitz authored`README.md` file describes - aim and background of the project (including the workflow DAG representation) - how to install requirements (including setting up a `conda` environment for the project) - how to execute the workflow run integration test - how to run the workflow on your own samples (including how to auto-generate required params from LabKey metadata) Additional minor changes: - minor changes in various test and related files, including updates of paths - root directory now includes subdirectory `runs/` for a user's workflow runs (contents not version-controlled)
test.sh 810 B
#!/bin/bash
# Tear down test environment
trap 'rm config.yaml samples.tsv && cd $user_dir' EXIT # quotes command is exected after script exits, regardless of exit status
# Set up test environment
set -eo pipefail # ensures that script exits at first command that exits with non-zero status
set -u # ensures that script exits when unset variables are used
set -x # facilitates debugging by printing out executed commands
user_dir=$PWD
script_dir="$(cd "$(dirname "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd)"
cd $script_dir
# Run tests
python "../../scripts/labkey_to_snakemake.py" \
--input_table="input_table.tsv" \
--input_dict="../../scripts/input_dict.tsv" \
--config_file="config.yaml" \
--samples_table="samples.tsv" \
--genomes_path="."
md5sum --check "expected_output.md5"