run_stubs.sh

#!/bin/bash

source scripts/nextflow_detached.sh
bcbio=$PWD/scripts/bcbio_nextgen.py

test_exit_status=0

rm -r work/*/*

echo "Test case 1: simple trio"
run_nextflow ../main.nf \
    -stub-run -profile stubs \
    --workflow variant-calling \
    --pipeline_project_id test_stub \
    --pipeline_project_version v1 \
    --ped_file assets/input_data/ped_files/batch_1.ped \
    --sample_sheet assets/input_data/sample_sheets/batch_1.tsv

test_exit_status=$(( $test_exit_status + $? ))

echo "Test case 2: MD5 errors"
run_nextflow ../main.nf \
    -stub-run -profile stubs \
    --workflow variant-calling \
    --pipeline_project_id test_stub_md5_errors \
    --pipeline_project_version v1 \
    --ped_file assets/input_data/ped_files/batch_2_md5_errors.ped \
    --sample_sheet assets/input_data/sample_sheets/batch_2_md5_errors.tsv

if [ $? == 0 ]
then
    test_exit_status=$(( $test_exit_status + 1 ))
fi

echo "Tests finished with exit status $test_exit_status"