#
# run normal mode
#
echo First run
$NXF_RUN | tee stdout

[[ `grep INFO .nextflow.log | grep -c 'Submitted process > align'` == 3 ]] || false
[[ `grep INFO .nextflow.log | grep -c 'Submitted process > my_combine'` == 1 ]] || false
cmp stdout .expected || false

[[ -f data/alpha.bai ]] || false
[[ -f data/alpha.bam ]] || false
[[ -f data/beta.bai ]] || false
[[ -f data/beta.bam ]] || false
[[ -f data/delta.bai ]] || false
[[ -f data/delta.bam ]] || false
[[ -L data/result.txt ]] || false
[[ -f more/data/result.txt ]] || false
[[ -f data/xxx/A ]] || false
[[ -f data/xxx/B ]] || false
[[ -f data/xxx/C ]] || false


#
# one more time to make sure 'overwrite' is fine
#
echo Second run
$NXF_RUN | tee stdout

[[ `grep INFO .nextflow.log | grep -c 'Submitted process > align'` == 3 ]] || false
[[ `grep INFO .nextflow.log | grep -c 'Submitted process > my_combine'` == 1 ]] || false
cmp stdout .expected || false

[[ -f data/alpha.bai ]] || false
[[ -f data/alpha.bam ]] || false
[[ -f data/beta.bai ]] || false
[[ -f data/beta.bam ]] || false
[[ -f data/delta.bai ]] || false
[[ -f data/delta.bam ]] || false
[[ -L data/result.txt ]] || false
[[ -f more/data/result.txt ]] || false
[[ -f data/xxx/A ]] || false
[[ -f data/xxx/B ]] || false
[[ -f data/xxx/C ]] || false


#
# clean & run resume mode
#
echo Third run
rm -rf data
rm -rf more/data

$NXF_RUN -resume | tee stdout

[[ `grep INFO .nextflow.log | grep -c 'Cached process > align'` == 3 ]] || false
[[ `grep INFO .nextflow.log | grep -c 'Cached process > my_combine'` == 1 ]] || false
cmp stdout .expected || false
[[ -f data/alpha.bai ]] || false
[[ -f data/alpha.bam ]] || false
[[ -f data/beta.bai ]] || false
[[ -f data/beta.bam ]] || false
[[ -f data/delta.bai ]] || false
[[ -f data/delta.bam ]] || false
[[ -L data/result.txt ]] || false
[[ -f more/data/result.txt ]] || false
#
# NOTE: on Mac when deleting an hard-link also the origin is removed
#
[[ -f data/xxx/A ]] || false
[[ -f data/xxx/B ]] || false
[[ -f data/xxx/C ]] || false