test.sh

#!/bin/bash

# Tear down test environment
cleanup () {
    rc=$?
    rm -rf .snakemake/
    rm -rf config.yaml
    rm -rf samples.tsv
    rm -rf logs
    cd $user_dir
    echo "Exit status: $rc"
}
trap cleanup EXIT

# 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/prepare_inputs.py" \
    --input-to-output-mapping="../../scripts/prepare_inputs.dict.tsv" \
    --resources-dir="../input_files" \
    --output-table="samples.tsv" \
    --config-file="config.yaml" \
    --multimappers='10' \
    --logo="../../images/logo.128px.png" \
    --output-dir="" \
    --no-process-paths \
    "input_table.tsv"


# Check if dry run completes
snakemake \
    --snakefile="../../Snakefile" \
    --configfile="config.yaml" \
    --dryrun \
    --verbose

md5sum --check "expected_output.md5"
# MD5 sums obtained with command:
# md5sum config.yaml samples.tsv > expected_output.md5