echo "Initial run"
$NXF_RUN --save_bam_bai | tee stdout

[[ $(grep INFO .nextflow.log | grep -c 'Submitted process > fastqc') == 3 ]] || false
[[ $(grep INFO .nextflow.log | grep -c 'Submitted process > align') == 3 ]] || false
[[ $(grep INFO .nextflow.log | grep -c 'Submitted process > quant') == 3 ]] || false
sed "s|"$(dirname "$(realpath "$0")")"||g" stdout > stdout.norm
cmp .expected-text stdout.norm || false

[[ -f results/log/sample1.fastqc.log ]] || false
[[ -f results/log/sample2.fastqc.log ]] || false
[[ -f results/log/sample3.fastqc.log ]] || false
[[ -f results/align/sample1.bai ]] || false
[[ -f results/align/sample1.bam ]] || false
[[ -f results/align/sample2.bai ]] || false
[[ -f results/align/sample2.bam ]] || false
[[ -f results/align/sample3.bai ]] || false
[[ -f results/align/sample3.bam ]] || false
[[ -L results/quant/sample1 ]] || false
[[ -L results/quant/sample2 ]] || false
[[ -L results/quant/sample3 ]] || false
[[ -f results/samples.csv ]] || false
[[ -f results/summary_report.html ]] || false
[[ -f results/summary_data/data.json ]] || false
[[ -f results/summary_data/fastqc.txt ]] || false


echo "Run again with overwrite enabled and JSON output"
$NXF_RUN -output-format json --save_bam_bai | tee stdout

[[ $(grep INFO .nextflow.log | grep -c 'Submitted process > fastqc') == 3 ]] || false
[[ $(grep INFO .nextflow.log | grep -c 'Submitted process > align') == 3 ]] || false
[[ $(grep INFO .nextflow.log | grep -c 'Submitted process > quant') == 3 ]] || false
sed "s|"$(dirname "$(realpath "$0")")"||g" stdout > stdout.norm
cmp .expected-json stdout.norm || false

[[ -f results/log/sample1.fastqc.log ]] || false
[[ -f results/log/sample2.fastqc.log ]] || false
[[ -f results/log/sample3.fastqc.log ]] || false
[[ -f results/align/sample1.bai ]] || false
[[ -f results/align/sample1.bam ]] || false
[[ -f results/align/sample2.bai ]] || false
[[ -f results/align/sample2.bam ]] || false
[[ -f results/align/sample3.bai ]] || false
[[ -f results/align/sample3.bam ]] || false
[[ -L results/quant/sample1 ]] || false
[[ -L results/quant/sample2 ]] || false
[[ -L results/quant/sample3 ]] || false
[[ -f results/samples.csv ]] || false
[[ -f results/summary_report.html ]] || false
[[ -f results/summary_data/data.json ]] || false
[[ -f results/summary_data/fastqc.txt ]] || false


echo "Run with some outputs disabled"
rm -rf results

$NXF_RUN -resume | tee stdout

[[ $(grep INFO .nextflow.log | grep -c 'Cached process > fastqc') == 3 ]] || false
[[ $(grep INFO .nextflow.log | grep -c 'Cached process > align') == 3 ]] || false
[[ $(grep INFO .nextflow.log | grep -c 'Cached process > quant') == 3 ]] || false

[[ -f results/log/sample1.fastqc.log ]] || false
[[ -f results/log/sample2.fastqc.log ]] || false
[[ -f results/log/sample3.fastqc.log ]] || false
[[ ! -e results/align ]] || false
[[ -L results/quant/sample1 ]] || false
[[ -L results/quant/sample2 ]] || false
[[ -L results/quant/sample3 ]] || false
[[ -f results/samples.csv ]] || false
[[ -f results/summary_report.html ]] || false
[[ -f results/summary_data/data.json ]] || false
[[ -f results/summary_data/fastqc.txt ]] || false


echo "Resumed run"
rm -rf results

$NXF_RUN --save_bam_bai -resume | tee stdout

[[ $(grep INFO .nextflow.log | grep -c 'Cached process > fastqc') == 3 ]] || false
[[ $(grep INFO .nextflow.log | grep -c 'Cached process > align') == 3 ]] || false
[[ $(grep INFO .nextflow.log | grep -c 'Cached process > quant') == 3 ]] || false

[[ -f results/log/sample1.fastqc.log ]] || false
[[ -f results/log/sample2.fastqc.log ]] || false
[[ -f results/log/sample3.fastqc.log ]] || false
[[ -f results/align/sample1.bai ]] || false
[[ -f results/align/sample1.bam ]] || false
[[ -f results/align/sample2.bai ]] || false
[[ -f results/align/sample2.bam ]] || false
[[ -f results/align/sample3.bai ]] || false
[[ -f results/align/sample3.bam ]] || false
[[ -L results/quant/sample1 ]] || false
[[ -L results/quant/sample2 ]] || false
[[ -L results/quant/sample3 ]] || false
[[ -f results/samples.csv ]] || false
[[ -f results/summary_report.html ]] || false
[[ -f results/summary_data/data.json ]] || false
[[ -f results/summary_data/fastqc.txt ]] || false