#!/bin/bash

output_folder=output/test11
nextflow main.nf -profile test,conda --algorithm star --reference `pwd`/test_data --output $output_folder
test -s $output_folder/TESTX_S1_L001.bam || { echo "Missing test 4 output file!"; exit 1; }
test -s $output_folder/TESTX_S1_L001.bam.bai || { echo "Missing test 4 output file!"; exit 1; }
test -s $output_folder/TESTX_S1_L001.fastp_stats.html || { echo "Missing test 4 output file!"; exit 1; }
test -s $output_folder/TESTX_S1_L001.fastp_stats.json || { echo "Missing test 4 output file!"; exit 1; }
test -s $output_folder/TESTX_S1_L002.bam || { echo "Missing test 4 output file!"; exit 1; }
test -s $output_folder/TESTX_S1_L002.bam.bai || { echo "Missing test 4 output file!"; exit 1; }
test -s $output_folder/TESTX_S1_L002.fastp_stats.html || { echo "Missing test 4 output file!"; exit 1; }
test -s $output_folder/TESTX_S1_L002.fastp_stats.json || { echo "Missing test 4 output file!"; exit 1; }