#
# run normal mode
#
echo First 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

[[ -f results/log/alpha.fastqc.log ]] || false
[[ -f results/log/beta.fastqc.log ]] || false
[[ -f results/log/delta.fastqc.log ]] || false
[[ -f results/align/alpha.bai ]] || false
[[ -f results/align/alpha.bam ]] || false
[[ -f results/align/beta.bai ]] || false
[[ -f results/align/beta.bam ]] || false
[[ -f results/align/delta.bai ]] || false
[[ -f results/align/delta.bam ]] || false
[[ -L results/quant/alpha ]] || false
[[ -L results/quant/beta ]] || false
[[ -L results/quant/delta ]] || false
[[ -f results/samples.csv ]] || false
[[ -f results/summary.txt ]] || false


#
# one more time to make sure 'overwrite' is fine
#
echo Second 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

[[ -f results/log/alpha.fastqc.log ]] || false
[[ -f results/log/beta.fastqc.log ]] || false
[[ -f results/log/delta.fastqc.log ]] || false
[[ -f results/align/alpha.bai ]] || false
[[ -f results/align/alpha.bam ]] || false
[[ -f results/align/beta.bai ]] || false
[[ -f results/align/beta.bam ]] || false
[[ -f results/align/delta.bai ]] || false
[[ -f results/align/delta.bam ]] || false
[[ -L results/quant/alpha ]] || false
[[ -L results/quant/beta ]] || false
[[ -L results/quant/delta ]] || false
[[ -f results/samples.csv ]] || false
[[ -f results/summary.txt ]] || false


#
# clean & run resume mode
#
echo Third 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/alpha.fastqc.log ]] || false
[[ -f results/log/beta.fastqc.log ]] || false
[[ -f results/log/delta.fastqc.log ]] || false
[[ -f results/align/alpha.bai ]] || false
[[ -f results/align/alpha.bam ]] || false
[[ -f results/align/beta.bai ]] || false
[[ -f results/align/beta.bam ]] || false
[[ -f results/align/delta.bai ]] || false
[[ -f results/align/delta.bam ]] || false
[[ -L results/quant/alpha ]] || false
[[ -L results/quant/beta ]] || false
[[ -L results/quant/delta ]] || false
[[ -f results/samples.csv ]] || false
[[ -f results/summary.txt ]] || false